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David M Stelly - One of the best experts on this subject based on the ideXlab platform.
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Effects of Interspecific Chromosome Substitution in Upland Cotton on Cottonseed Micronutrients.
Plants (Basel Switzerland), 2020Co-Authors: Nacer Bellaloui, Sukumar Saha, Johnie N. Jenkins, Jennifer L. Tonos, Jodi A. Scheffler, Jack C. Mccarty, David M StellyAbstract:Micronutrients are essential for plant growth and development, and important for human health nutrition and livestock feed. Therefore, the discovery of novel germplasm with significant variability or higher micronutrients content in crop seeds is critical. Currently, there is no information available on the effects of Chromosome or Chromosome arm Substitution in cotton on cottonseed micronutrients. Thus, the objective of this study was to evaluate the effects of Chromosome or Chromosome arm Substitution on the variability and levels of micronutrients B, Fe, Cu, Zn, Mn, and Ni in cottonseed from Chromosome Substitution (CS) cotton lines. Our hypothesis was that interspecific Chromosome Substitution in cotton can affect cottonseed micronutrients content, resulting in significant differences and variabilities of these nutrients among CS lines and between CS lines and the controls. Nine CS lines were grown in two-field experiments at two locations (in 2013 in South Carolina, USA; and in 2014 in Mississippi, USA). TM-1 (the recurrent parent of the CS line) and AM UA48 (cultivar) were used as control. The results showed significant variability among CS lines compared to the controls AM UA48 and TM-1. For example, in South Carolina (SC), B concentration in cottonseed ranged from 10.35 mg kg−1 in CS-M02 to 13.67 mg kg−1 in CS-T04. The concentration of Cu ranged from 4.81 mg kg−1 in CS-B08sh to 7.65 mg kg−1 in CS-T02, and CS-T02 was higher than both controls. The concentration of Fe ranged from 36.09 mg kg−1 to 56.69 mg kg−1 (an increase up to 57%), and six CS lines (CS-B02, CS-B08sh, CS-M02, CS-M04, CS-T02, and CS-T04) had higher concentration than both controls in 2013. In 2014 at the Mississippi location (MS), similar observation was found with CS lines for micronutrients content. The CS lines with higher concentrations of these micronutrients can be used as a genetic tool toward QTL identification for desired seed traits because these lines are genetically similar with TM-1, except the substituted Chromosome or Chromosome segment pairs from the alien species. Chromosome Substitution provides an effective means for upland cotton improvement by targeted interspecific introgression, yielding CS lines that facilitate trait discovery, such as seed micronutritional qualities, due to increased isogenicity and markedly reduced complexity from epistatic interactions with non-target alien Chromosomes. The positive correlation between B, Cu, and Fe at both locations, between Ni and Mn, between Zn and Cu, and between Zn and Ni at both locations signify the importance of a good agricultural and fertilizer management of these nutrients to maintain higher cottonseed nutrient content.
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Morph-physiological responses of cotton interspecific Chromosome Substitution lines to low temperature and drought stresses
Euphytica, 2018Co-Authors: Akanksha Awasthi, Sukumar Saha, K. Raja Reddy, Johnie N. Jenkins, David M StellyAbstract:Limited knowledge about genetic and physiological traits associated with drought and low temperature stresses and narrow genetic diversity in Upland cotton (Gossypium hirsutum L.) are serious impediments in its genetic improvement. The objectives of this research were to determine the genetic and physiological traits associated with drought and low temperature effects and to identify chromosomal effects on these traits using Chromosome Substitution (CS) lines from three alien species of Gossypium, G. barbadense, G. tomentosum, and G. mustelinum, respectively. Two experiments were conducted to study low temperature and drought stress effects during seedling emergence and early growth stages in 21 cotton CS-lines with parent, Texas Marker (TM)-1. In Experiment I, plants were grown at optimum (30/22 °C) and low (22/14 °C) temperature conditions under optimum water and nutrient conditions. In Experiment II, plants were grown at optimum water (soil moisture content of 0.167 m3 m−3) and in drought (soil moisture content 0.105 m3 m−3) conditions under optimum temperature conditions. Above- and below-ground growth traits including several root traits of the CS lines were assessed at 25 days after sowing. The findings suggest which substituted Chromosome or Chromosome segment from the alien species likely harbors one or more genes for higher and lower tolerance to low temperature, respectively. CS-T04 and CSB08sh showed higher and lower tolerance to low temperature, respectively and CS-T04 and CS-B22sh showed higher and lower tolerance, respectively, to drought. CS lines are valuable analytical tool and useful genetic resources for targeted exploitation of beneficial genes for drought and low temperature stresses in Upland cotton.
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analysis of root knot nematode and fusarium wilt disease resistance in cotton gossypium spp using Chromosome Substitution lines from two alien species
Genetica, 2016Co-Authors: Mauricio Ulloa, David M Stelly, Sukumar Saha, J N Jenkins, Congli Wang, Robert B Hutmacher, John J Burke, Philip A RobertsAbstract:Chromosome Substitution (CS) lines in plants are a powerful genetic resource for analyzing the contribution of Chromosome segments to phenotypic variance. In this study, a series of interspecific cotton (Gossypium spp.) CS lines were used to identify a new germplasm resource, and to validate chromosomal regions and favorable alleles associated with nematode or fungal disease resistance traits. The CS lines were developed in the G. hirsutum L. TM-1 background with Chromosome or Chromosome segment Substitutions from G. barbadense L. Pima 3-79 or G. tomentosum. Root-knot nematode (Meloidogyne incognita) and fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) (races 1 and 4) resistance alleles and quantitative trait loci (QTL) previously placed on cotton Chromosomes using SSR markers in two interspecific recombinant inbred line populations were chosen for testing. Phenotypic responses of increased resistance or susceptibility in controlled inoculation and infested field assays confirmed the resistance QTLs, based on Substitution with the positive or negative allele for resistance. Lines CS-B22Lo, CS-B04, and CS-B18 showed high resistance to nematode root-galling, confirming QTLs on Chromosomes 4 and 22 (long arm) with resistance alleles from Pima 3-79. Line CS-B16 had less fusarium race 1-induced vascular root staining and higher percent survival than the TM-1 parent, confirming a major resistance QTL on Chromosome 16. Lines CS-B(17-11) and CS-B17 had high fusarium race 4 vascular symptoms and low survival due to susceptible alleles introgressed from Pima 3-79, confirming the localization on Chromosome 17 of an identified QTL with resistance alleles from TM1 and other resistant lines. Analyses validated regions on Chromosomes 11, 16, and 17 harboring nematode and fusarium wilt resistance genes and demonstrated the value of CS lines as both a germplasm resource for breeding programs and as a powerful genetic analysis tool for determining QTL effects for disease resistance. CS lines carrying small alien Chromosome segments with favorable QTL alleles could be used for effective introgression of biotic stress resistance or many other desirable traits by targeting gene interactions and reducing linkage drag effects.
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Molecular confirmation of Gossypium hirsutum Chromosome Substitution lines
Euphytica, 2015Co-Authors: Sukumar Saha, David M Stelly, Johnie N. Jenkins, Dwaine A. Raska, Shivapriya Manchali, Osman A. Gutiérrez, Abdusalom K. Makamov, Mirzakamol S. Ayubov, Dewayne Deng, Ibrokhim Y. AbdurakhmonovAbstract:The primary gene pool for tetraploid cotton species includes Gossypium hirsutum L., as well as the other four 2n = 52 species of Gossypium (G. barbadense, G. mustellinum, G. tomentosum and G. darwinii). To help overcome barriers to effective introgression, we have developed a number of alien Chromosome Substitution (CS) lines from G. barbadense, G. mustellinum and G. tomentosum, most of which are nearly isogenic to the inbred ‘Texas Marker-1’, a genetic standard. At the time CS line development was initiated, molecular markers did not exist for some CS lines, and most of these lines were developed based on cytological analysis without using any marker-based testing. Here we report on tests with SSR markers from one ore more linkage maps specific to the substituted Chromosome or Chromosome segment from one or more linkage maps to assess the constitution and genetic identity of the CS lines. The specific objective of this paper is to report on the genetic identity of the CS lines using SSR markers and some special characteristics associated with some of the CS lines. We used Chromosome-specific SSR markers following standard methods of DNA extraction, PCR and according to manufacturer’s protocol on ABI Genetic Analyzer 3130xl to confirm the identity of the introgressed alien Chromosome or Chromosome segments in the CS lines. For most CS lines and most mapped markers, the observed SSR profiles were concordant with expectations as per the results of cytological analysis. For a minority of markers and lines, however, the results were discordant; these markers, linkage groups, and CS lines will be further investigated to understand and define their genetic identity for use as breeding resources. Interspecific germplasm introgression can be useful for genetic improvement of Upland cotton. However, such efforts are constrained by genetic incompatibilities between the species. Our results document for the first time the development of CS lines from G. tomentosum and G. mustelinum. These CS lines will open a new paradigm in cotton breeding program by providing a tool for introgression of useful genes from wild and unadapted species in the genetic improvement of Upland cotton.
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BREEDING AND GENETICS Hypoaneuploid Chromosome Substitution F1 Hybrids of Gossypium hirsutum L. x G. mustelinum Miers ex Watt
2013Co-Authors: Sukumar Saha, David M Stelly, Dwaine A. Raska, Shivapriya Manchali, Osman A. GutiérrezAbstract:The infusion of new genetic diversity fr om related species into domesticated types of cotton (Gossypium hirsutum L.) will greatly increase opportunities for genetic improvement. We report here the development of the aneuploid F1 Chromosome Substitution stocks in G. hirsutum for whole Chromosomes and Chromosome arms of G. mustelinum Miers ex Watt. These hypoaneuploid interspecific Chromosome Substitution stocks are an additional genetic resource for localization of genomic sequences, marker development, definition of linkage groups, and validation of genome maps. Hypoaneuploid plants that lack specific Chromosomes or arms were detected by analysis of phenotypic syndromes and conventional meiotic metaphaseI configuration analysis of acetocarmine-stained microsporocytes (“pollen mother cells”), as well as by deletion analysis with Chromosome specific SSR markers. Here, we report the development of 25 such hypoaneuploid hybrids, including 13 monosomic hybrids, each missing a different G. hirsutum Chromosome (Chromosome 1, 2, 4, 6, 7, 9, 10, 12, 16, 17, 18, 20, and 25, respectively), and 12 monotelodisomic (acrocentric) hybrids (Te05Lo, Te08Lo, Te11Lo, Te11sh, Te12Lo, Te14Lo, Te15Lo, Te20Lo, Te20sh, Te22Lo, Te22sh, and Te26sh) that are deficient for the respective distal segment of opposing G. hirsutum arms 5sh, 8sh, 11sh, 11Lo, 12sh, 14sh, 15sh, 20sh, 20Lo, 22sh, 22Lo, and 26Lo. Each of the interspecific F 1s reported here is a major step toward a development of the respective backcross disomic Substitution line. Such lines are individually and collectively powerful resources for targeted germplasm introgression, genetic dissection, and genetic improvement of complex traits.
Ann Corey - One of the best experts on this subject based on the ideXlab platform.
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association mapping of plant height yield and yield stability in recombinant Chromosome Substitution lines rcsls using hordeum vulgare subsp spontaneum as a source of donor alleles in a hordeum vulgare subsp vulgare background
Molecular Breeding, 2009Co-Authors: Luis Inostroza, Ivan Matus, Patrick M Hayes, Alejandro Del Pozo, Dalma Castillo, Stephen Machado, Ann CoreyAbstract:Grain yield and plant height of 80 recombinant Chromosome Substitution lines (RCSLs) of barley were measured in six environments with contrasting available moisture profiles. Two environments were in OR, USA (Moro and Pendleton) during one growing season (2004), and four in Chile (Cauquenes and Santa Rosa) during two growing seasons (2004/2005 and 2007/2008). From the yield data obtained in the different environments, yield adaptability (Finlay–Wilkinson slope) and stability (deviations from regression) were calculated. Two commercial cultivars (Harrington and Baronesse) were used as checks in all environments. Marker-quantitative trait associations were identified using 47 simple sequence repeats (SSRs) and the general linear model (GLM) implemented in TASSEL. The mean plant height and grain yield of the 80 RCSLs differed greatly across environments, reflecting differences in water availability. In all environments, there were significant differences (P < 0.05) in grain yield among RCSLs. There was also abundant variation in yield adaptability, indicating a differential response of the RCSLs to environmental conditions across environments. Using principal component analysis, it was possible to identify genotypes with better agronomic performance than the recurrent parent cv. Harrington. The association analysis revealed 21 chromosomal regions that were highly correlated with differences in grain yield, plant height and/or yield adaptability (Finlay–Wilkinson slope). In approximately one-fourth of the cases, the H. spontaneum donor contributed favorable alleles. The associations were referenced to the quantitative trait loci (QTL) for the same traits reported in the literature.
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Association mapping of plant height, yield, and yield stability in recombinant Chromosome Substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background
Molecular Breeding, 2009Co-Authors: Luis Inostroza, Ivan Matus, Alejandro Del Pozo, Dalma Castillo, Patrick Hayes, Stephen Machado, Ann CoreyAbstract:Grain yield and plant height of 80 recombinant Chromosome Substitution lines (RCSLs) of barley were measured in six environments with contrasting available moisture profiles. Two environments were in OR, USA (Moro and Pendleton) during one growing season (2004), and four in Chile (Cauquenes and Santa Rosa) during two growing seasons (2004/2005 and 2007/2008). From the yield data obtained in the different environments, yield adaptability (Finlay–Wilkinson slope) and stability (deviations from regression) were calculated. Two commercial cultivars (Harrington and Baronesse) were used as checks in all environments. Marker-quantitative trait associations were identified using 47 simple sequence repeats (SSRs) and the general linear model (GLM) implemented in TASSEL. The mean plant height and grain yield of the 80 RCSLs differed greatly across environments, reflecting differences in water availability. In all environments, there were significant differences ( P
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development and characterization of recombinant Chromosome Substitution lines rcsls using hordeum vulgare subsp spontaneum as a source of donor alleles in a hordeum vulgare subsp vulgare background
Genome, 2003Co-Authors: Ivan Matus, Kazuhiro Sato, Ann Corey, Tanya Filichkin, Patrick M Hayes, M I Vales, J G Kling, Oscar Rieralizarazu, W Powell, Robbie WaughAbstract:The ancestor of barley (Hordeum vulgare subsp. spontaneum) may be a source of novel alleles for crop improvement. We developed a set of recombinant Chromosome Substitution lines (RCSLs) using an accession of H. vulgare subsp. spontaneum (Caesarea 26-24, from Israel) as the donor and Hordeum vulgare subsp. vulgare 'Harrington' (the North American malting quality standard) as the recurrent parent via two backcrosses to the recurrent parent, followed by six generations of selfing. Here we report (i) the genomic architecture of the RCSLs, as inferred by simple sequence repeat (SSR) markers, and (ii) the effects of H. vulgare subsp. spontaneum genome segment introgressions in terms of three classes of phenotypes: inflorescence yield components, malting quality traits, and domestication traits. Significant differences among the RCSLs were detected for all phenotypes measured. The phenotypic effects of the introgressions were assessed using association analysis, and these were referenced to quantitative trait lo...
Johnie N. Jenkins - One of the best experts on this subject based on the ideXlab platform.
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Effects of Interspecific Chromosome Substitution in Upland Cotton on Cottonseed Micronutrients.
Plants (Basel Switzerland), 2020Co-Authors: Nacer Bellaloui, Sukumar Saha, Johnie N. Jenkins, Jennifer L. Tonos, Jodi A. Scheffler, Jack C. Mccarty, David M StellyAbstract:Micronutrients are essential for plant growth and development, and important for human health nutrition and livestock feed. Therefore, the discovery of novel germplasm with significant variability or higher micronutrients content in crop seeds is critical. Currently, there is no information available on the effects of Chromosome or Chromosome arm Substitution in cotton on cottonseed micronutrients. Thus, the objective of this study was to evaluate the effects of Chromosome or Chromosome arm Substitution on the variability and levels of micronutrients B, Fe, Cu, Zn, Mn, and Ni in cottonseed from Chromosome Substitution (CS) cotton lines. Our hypothesis was that interspecific Chromosome Substitution in cotton can affect cottonseed micronutrients content, resulting in significant differences and variabilities of these nutrients among CS lines and between CS lines and the controls. Nine CS lines were grown in two-field experiments at two locations (in 2013 in South Carolina, USA; and in 2014 in Mississippi, USA). TM-1 (the recurrent parent of the CS line) and AM UA48 (cultivar) were used as control. The results showed significant variability among CS lines compared to the controls AM UA48 and TM-1. For example, in South Carolina (SC), B concentration in cottonseed ranged from 10.35 mg kg−1 in CS-M02 to 13.67 mg kg−1 in CS-T04. The concentration of Cu ranged from 4.81 mg kg−1 in CS-B08sh to 7.65 mg kg−1 in CS-T02, and CS-T02 was higher than both controls. The concentration of Fe ranged from 36.09 mg kg−1 to 56.69 mg kg−1 (an increase up to 57%), and six CS lines (CS-B02, CS-B08sh, CS-M02, CS-M04, CS-T02, and CS-T04) had higher concentration than both controls in 2013. In 2014 at the Mississippi location (MS), similar observation was found with CS lines for micronutrients content. The CS lines with higher concentrations of these micronutrients can be used as a genetic tool toward QTL identification for desired seed traits because these lines are genetically similar with TM-1, except the substituted Chromosome or Chromosome segment pairs from the alien species. Chromosome Substitution provides an effective means for upland cotton improvement by targeted interspecific introgression, yielding CS lines that facilitate trait discovery, such as seed micronutritional qualities, due to increased isogenicity and markedly reduced complexity from epistatic interactions with non-target alien Chromosomes. The positive correlation between B, Cu, and Fe at both locations, between Ni and Mn, between Zn and Cu, and between Zn and Ni at both locations signify the importance of a good agricultural and fertilizer management of these nutrients to maintain higher cottonseed nutrient content.
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Morph-physiological responses of cotton interspecific Chromosome Substitution lines to low temperature and drought stresses
Euphytica, 2018Co-Authors: Akanksha Awasthi, Sukumar Saha, K. Raja Reddy, Johnie N. Jenkins, David M StellyAbstract:Limited knowledge about genetic and physiological traits associated with drought and low temperature stresses and narrow genetic diversity in Upland cotton (Gossypium hirsutum L.) are serious impediments in its genetic improvement. The objectives of this research were to determine the genetic and physiological traits associated with drought and low temperature effects and to identify chromosomal effects on these traits using Chromosome Substitution (CS) lines from three alien species of Gossypium, G. barbadense, G. tomentosum, and G. mustelinum, respectively. Two experiments were conducted to study low temperature and drought stress effects during seedling emergence and early growth stages in 21 cotton CS-lines with parent, Texas Marker (TM)-1. In Experiment I, plants were grown at optimum (30/22 °C) and low (22/14 °C) temperature conditions under optimum water and nutrient conditions. In Experiment II, plants were grown at optimum water (soil moisture content of 0.167 m3 m−3) and in drought (soil moisture content 0.105 m3 m−3) conditions under optimum temperature conditions. Above- and below-ground growth traits including several root traits of the CS lines were assessed at 25 days after sowing. The findings suggest which substituted Chromosome or Chromosome segment from the alien species likely harbors one or more genes for higher and lower tolerance to low temperature, respectively. CS-T04 and CSB08sh showed higher and lower tolerance to low temperature, respectively and CS-T04 and CS-B22sh showed higher and lower tolerance, respectively, to drought. CS lines are valuable analytical tool and useful genetic resources for targeted exploitation of beneficial genes for drought and low temperature stresses in Upland cotton.
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Molecular confirmation of Gossypium hirsutum Chromosome Substitution lines
Euphytica, 2015Co-Authors: Sukumar Saha, David M Stelly, Johnie N. Jenkins, Dwaine A. Raska, Shivapriya Manchali, Osman A. Gutiérrez, Abdusalom K. Makamov, Mirzakamol S. Ayubov, Dewayne Deng, Ibrokhim Y. AbdurakhmonovAbstract:The primary gene pool for tetraploid cotton species includes Gossypium hirsutum L., as well as the other four 2n = 52 species of Gossypium (G. barbadense, G. mustellinum, G. tomentosum and G. darwinii). To help overcome barriers to effective introgression, we have developed a number of alien Chromosome Substitution (CS) lines from G. barbadense, G. mustellinum and G. tomentosum, most of which are nearly isogenic to the inbred ‘Texas Marker-1’, a genetic standard. At the time CS line development was initiated, molecular markers did not exist for some CS lines, and most of these lines were developed based on cytological analysis without using any marker-based testing. Here we report on tests with SSR markers from one ore more linkage maps specific to the substituted Chromosome or Chromosome segment from one or more linkage maps to assess the constitution and genetic identity of the CS lines. The specific objective of this paper is to report on the genetic identity of the CS lines using SSR markers and some special characteristics associated with some of the CS lines. We used Chromosome-specific SSR markers following standard methods of DNA extraction, PCR and according to manufacturer’s protocol on ABI Genetic Analyzer 3130xl to confirm the identity of the introgressed alien Chromosome or Chromosome segments in the CS lines. For most CS lines and most mapped markers, the observed SSR profiles were concordant with expectations as per the results of cytological analysis. For a minority of markers and lines, however, the results were discordant; these markers, linkage groups, and CS lines will be further investigated to understand and define their genetic identity for use as breeding resources. Interspecific germplasm introgression can be useful for genetic improvement of Upland cotton. However, such efforts are constrained by genetic incompatibilities between the species. Our results document for the first time the development of CS lines from G. tomentosum and G. mustelinum. These CS lines will open a new paradigm in cotton breeding program by providing a tool for introgression of useful genes from wild and unadapted species in the genetic improvement of Upland cotton.
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Genetic effects of nine Gossypium barbadense L. Chromosome Substitution lines in top crosses with five elite Upland cotton G. hirsutum L. cultivars
Euphytica, 2012Co-Authors: Johnie N. Jenkins, Jack C. Mccarty, Jixiang Wu, Russell Hayes, David StellyAbstract:Crosses between Gossypium barbadense L and Gossypium hirsutum L. (Upland cotton) have produced limited success in introgressing fiber quality genes into the latter. Chromosome Substitution lines (CSBL) have complete Chromosomes or Chromosome arms from G. barbadense , line 3-79, substituted for the corresponding Chromosome or arms in G. hirsutum in a near isogenic background of TM-1. We top crossed nine CSBL and their parents (TM-1 and 3-79) with five cultivars. Parental lines and their F_2 populations were evaluated in four environments for agronomic and fiber quality traits. The CSBL and their F_2 hybrids showed wide ranges for both agronomic and fiber traits of economic importance. Genetic analysis showed that additive variances were larger than dominance variances for lint percentage, boll weight, lint yield, fiber length, strength, elongation, micronaire, and yellowness; whereas, dominance variances were larger than additive variances only for uniformity of fiber length and equal for fiber reflectance. For all traits, except boll weight and lint yield, significant additive effects of one or more Chromosomes from 3-79 in TM-1 background were greater than the corresponding TM-1 Chromosome. In addition, we identified specific Chromosomes from G. barbadense (3-79) that carry alleles for improvements in specific fiber quality traits in Upland cotton. Favorable additive effects of individual Chromosomes or Chromosome segments from 3-79 relative to corresponding Chromosomes or Chromosomes segments from TM-1 were identified in this study as follows: Lint percentage, Chromosome/arms 10, 16-15; longer fibers, Chromosome/arms 01, 11sh, 26Lo; more uniform fibers, Chromosomes/arms 01, 11sh, 10, 17-11; stronger fibers, Chromosome/arms 01, 11sh, 12sh, 26Lo, 17-11; fiber elongation, Chromosomes/arms 01, 11sh, 26Lo, 10, 17-11; reduced fiber micronaire, Chromosome/arms 01, 12sh, 4-15, 16-15, 17-11; fibers with more reflectance, Chromosome/arms 10, 4-15, 16-15, 17-11; fiber with less yellowness, Chromosome arms 4-15, 17-11. Based on the present study, we concluded that by using CSBL, favorable fiber quality alleles can be introgressed into Upland cotton, thus greatly improving the breeder’s ability for improvement of Upland cotton for a variety of traits. These data should provide useful genetic information to the cotton breeding industry at large.
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Genetic effects of individual Chromosomes in cotton cultivars detected by using Chromosome Substitution lines as genetic probes
Genetica, 2010Co-Authors: Johnie N. Jenkins, Jack C. Mccarty, Sukumar SahaAbstract:Determination of Chromosomes or Chromosome arms with desirable genes in different inbred lines and/or crosses should provide useful genetic information for crop improvement. In this study, we applied a modified additive-dominance model to analyze a data set of 13 cotton Chromosome Substitution lines and their recurrent parent TM-1, five commercial cultivars, and their 70 F_2 hybrids. The Chromosome additive and dominance variance components for eight agronomic and fiber traits were determined. On average, each Chromosome or Chromosome arm was associated with 6.5 traits in terms of additive and/or dominance effects. The Chromosomes or Chromosome arms, which contributed significant additive variances for the traits investigated, included 2, 16, 18, 25, 5sh (short arm), 14sh, 15sh, 22sh, and 22Lo (long arm). Chromosome additive effects were also predicted in this study. The results showed that CS-B 25 was favorably associated with several fiber traits, while FM966 was favorably associated with both yield and fiber traits with alleles on multiple Chromosomes or Chromosome arms. Thus, this study should provide valuable genetic information on pure line development for several improved traits such as yield and fiber quality.
Sukumar Saha - One of the best experts on this subject based on the ideXlab platform.
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Effects of Interspecific Chromosome Substitution in Upland Cotton on Cottonseed Micronutrients.
Plants (Basel Switzerland), 2020Co-Authors: Nacer Bellaloui, Sukumar Saha, Johnie N. Jenkins, Jennifer L. Tonos, Jodi A. Scheffler, Jack C. Mccarty, David M StellyAbstract:Micronutrients are essential for plant growth and development, and important for human health nutrition and livestock feed. Therefore, the discovery of novel germplasm with significant variability or higher micronutrients content in crop seeds is critical. Currently, there is no information available on the effects of Chromosome or Chromosome arm Substitution in cotton on cottonseed micronutrients. Thus, the objective of this study was to evaluate the effects of Chromosome or Chromosome arm Substitution on the variability and levels of micronutrients B, Fe, Cu, Zn, Mn, and Ni in cottonseed from Chromosome Substitution (CS) cotton lines. Our hypothesis was that interspecific Chromosome Substitution in cotton can affect cottonseed micronutrients content, resulting in significant differences and variabilities of these nutrients among CS lines and between CS lines and the controls. Nine CS lines were grown in two-field experiments at two locations (in 2013 in South Carolina, USA; and in 2014 in Mississippi, USA). TM-1 (the recurrent parent of the CS line) and AM UA48 (cultivar) were used as control. The results showed significant variability among CS lines compared to the controls AM UA48 and TM-1. For example, in South Carolina (SC), B concentration in cottonseed ranged from 10.35 mg kg−1 in CS-M02 to 13.67 mg kg−1 in CS-T04. The concentration of Cu ranged from 4.81 mg kg−1 in CS-B08sh to 7.65 mg kg−1 in CS-T02, and CS-T02 was higher than both controls. The concentration of Fe ranged from 36.09 mg kg−1 to 56.69 mg kg−1 (an increase up to 57%), and six CS lines (CS-B02, CS-B08sh, CS-M02, CS-M04, CS-T02, and CS-T04) had higher concentration than both controls in 2013. In 2014 at the Mississippi location (MS), similar observation was found with CS lines for micronutrients content. The CS lines with higher concentrations of these micronutrients can be used as a genetic tool toward QTL identification for desired seed traits because these lines are genetically similar with TM-1, except the substituted Chromosome or Chromosome segment pairs from the alien species. Chromosome Substitution provides an effective means for upland cotton improvement by targeted interspecific introgression, yielding CS lines that facilitate trait discovery, such as seed micronutritional qualities, due to increased isogenicity and markedly reduced complexity from epistatic interactions with non-target alien Chromosomes. The positive correlation between B, Cu, and Fe at both locations, between Ni and Mn, between Zn and Cu, and between Zn and Ni at both locations signify the importance of a good agricultural and fertilizer management of these nutrients to maintain higher cottonseed nutrient content.
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Morph-physiological responses of cotton interspecific Chromosome Substitution lines to low temperature and drought stresses
Euphytica, 2018Co-Authors: Akanksha Awasthi, Sukumar Saha, K. Raja Reddy, Johnie N. Jenkins, David M StellyAbstract:Limited knowledge about genetic and physiological traits associated with drought and low temperature stresses and narrow genetic diversity in Upland cotton (Gossypium hirsutum L.) are serious impediments in its genetic improvement. The objectives of this research were to determine the genetic and physiological traits associated with drought and low temperature effects and to identify chromosomal effects on these traits using Chromosome Substitution (CS) lines from three alien species of Gossypium, G. barbadense, G. tomentosum, and G. mustelinum, respectively. Two experiments were conducted to study low temperature and drought stress effects during seedling emergence and early growth stages in 21 cotton CS-lines with parent, Texas Marker (TM)-1. In Experiment I, plants were grown at optimum (30/22 °C) and low (22/14 °C) temperature conditions under optimum water and nutrient conditions. In Experiment II, plants were grown at optimum water (soil moisture content of 0.167 m3 m−3) and in drought (soil moisture content 0.105 m3 m−3) conditions under optimum temperature conditions. Above- and below-ground growth traits including several root traits of the CS lines were assessed at 25 days after sowing. The findings suggest which substituted Chromosome or Chromosome segment from the alien species likely harbors one or more genes for higher and lower tolerance to low temperature, respectively. CS-T04 and CSB08sh showed higher and lower tolerance to low temperature, respectively and CS-T04 and CS-B22sh showed higher and lower tolerance, respectively, to drought. CS lines are valuable analytical tool and useful genetic resources for targeted exploitation of beneficial genes for drought and low temperature stresses in Upland cotton.
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analysis of root knot nematode and fusarium wilt disease resistance in cotton gossypium spp using Chromosome Substitution lines from two alien species
Genetica, 2016Co-Authors: Mauricio Ulloa, David M Stelly, Sukumar Saha, J N Jenkins, Congli Wang, Robert B Hutmacher, John J Burke, Philip A RobertsAbstract:Chromosome Substitution (CS) lines in plants are a powerful genetic resource for analyzing the contribution of Chromosome segments to phenotypic variance. In this study, a series of interspecific cotton (Gossypium spp.) CS lines were used to identify a new germplasm resource, and to validate chromosomal regions and favorable alleles associated with nematode or fungal disease resistance traits. The CS lines were developed in the G. hirsutum L. TM-1 background with Chromosome or Chromosome segment Substitutions from G. barbadense L. Pima 3-79 or G. tomentosum. Root-knot nematode (Meloidogyne incognita) and fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) (races 1 and 4) resistance alleles and quantitative trait loci (QTL) previously placed on cotton Chromosomes using SSR markers in two interspecific recombinant inbred line populations were chosen for testing. Phenotypic responses of increased resistance or susceptibility in controlled inoculation and infested field assays confirmed the resistance QTLs, based on Substitution with the positive or negative allele for resistance. Lines CS-B22Lo, CS-B04, and CS-B18 showed high resistance to nematode root-galling, confirming QTLs on Chromosomes 4 and 22 (long arm) with resistance alleles from Pima 3-79. Line CS-B16 had less fusarium race 1-induced vascular root staining and higher percent survival than the TM-1 parent, confirming a major resistance QTL on Chromosome 16. Lines CS-B(17-11) and CS-B17 had high fusarium race 4 vascular symptoms and low survival due to susceptible alleles introgressed from Pima 3-79, confirming the localization on Chromosome 17 of an identified QTL with resistance alleles from TM1 and other resistant lines. Analyses validated regions on Chromosomes 11, 16, and 17 harboring nematode and fusarium wilt resistance genes and demonstrated the value of CS lines as both a germplasm resource for breeding programs and as a powerful genetic analysis tool for determining QTL effects for disease resistance. CS lines carrying small alien Chromosome segments with favorable QTL alleles could be used for effective introgression of biotic stress resistance or many other desirable traits by targeting gene interactions and reducing linkage drag effects.
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Molecular confirmation of Gossypium hirsutum Chromosome Substitution lines
Euphytica, 2015Co-Authors: Sukumar Saha, David M Stelly, Johnie N. Jenkins, Dwaine A. Raska, Shivapriya Manchali, Osman A. Gutiérrez, Abdusalom K. Makamov, Mirzakamol S. Ayubov, Dewayne Deng, Ibrokhim Y. AbdurakhmonovAbstract:The primary gene pool for tetraploid cotton species includes Gossypium hirsutum L., as well as the other four 2n = 52 species of Gossypium (G. barbadense, G. mustellinum, G. tomentosum and G. darwinii). To help overcome barriers to effective introgression, we have developed a number of alien Chromosome Substitution (CS) lines from G. barbadense, G. mustellinum and G. tomentosum, most of which are nearly isogenic to the inbred ‘Texas Marker-1’, a genetic standard. At the time CS line development was initiated, molecular markers did not exist for some CS lines, and most of these lines were developed based on cytological analysis without using any marker-based testing. Here we report on tests with SSR markers from one ore more linkage maps specific to the substituted Chromosome or Chromosome segment from one or more linkage maps to assess the constitution and genetic identity of the CS lines. The specific objective of this paper is to report on the genetic identity of the CS lines using SSR markers and some special characteristics associated with some of the CS lines. We used Chromosome-specific SSR markers following standard methods of DNA extraction, PCR and according to manufacturer’s protocol on ABI Genetic Analyzer 3130xl to confirm the identity of the introgressed alien Chromosome or Chromosome segments in the CS lines. For most CS lines and most mapped markers, the observed SSR profiles were concordant with expectations as per the results of cytological analysis. For a minority of markers and lines, however, the results were discordant; these markers, linkage groups, and CS lines will be further investigated to understand and define their genetic identity for use as breeding resources. Interspecific germplasm introgression can be useful for genetic improvement of Upland cotton. However, such efforts are constrained by genetic incompatibilities between the species. Our results document for the first time the development of CS lines from G. tomentosum and G. mustelinum. These CS lines will open a new paradigm in cotton breeding program by providing a tool for introgression of useful genes from wild and unadapted species in the genetic improvement of Upland cotton.
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BREEDING AND GENETICS Hypoaneuploid Chromosome Substitution F1 Hybrids of Gossypium hirsutum L. x G. mustelinum Miers ex Watt
2013Co-Authors: Sukumar Saha, David M Stelly, Dwaine A. Raska, Shivapriya Manchali, Osman A. GutiérrezAbstract:The infusion of new genetic diversity fr om related species into domesticated types of cotton (Gossypium hirsutum L.) will greatly increase opportunities for genetic improvement. We report here the development of the aneuploid F1 Chromosome Substitution stocks in G. hirsutum for whole Chromosomes and Chromosome arms of G. mustelinum Miers ex Watt. These hypoaneuploid interspecific Chromosome Substitution stocks are an additional genetic resource for localization of genomic sequences, marker development, definition of linkage groups, and validation of genome maps. Hypoaneuploid plants that lack specific Chromosomes or arms were detected by analysis of phenotypic syndromes and conventional meiotic metaphaseI configuration analysis of acetocarmine-stained microsporocytes (“pollen mother cells”), as well as by deletion analysis with Chromosome specific SSR markers. Here, we report the development of 25 such hypoaneuploid hybrids, including 13 monosomic hybrids, each missing a different G. hirsutum Chromosome (Chromosome 1, 2, 4, 6, 7, 9, 10, 12, 16, 17, 18, 20, and 25, respectively), and 12 monotelodisomic (acrocentric) hybrids (Te05Lo, Te08Lo, Te11Lo, Te11sh, Te12Lo, Te14Lo, Te15Lo, Te20Lo, Te20sh, Te22Lo, Te22sh, and Te26sh) that are deficient for the respective distal segment of opposing G. hirsutum arms 5sh, 8sh, 11sh, 11Lo, 12sh, 14sh, 15sh, 20sh, 20Lo, 22sh, 22Lo, and 26Lo. Each of the interspecific F 1s reported here is a major step toward a development of the respective backcross disomic Substitution line. Such lines are individually and collectively powerful resources for targeted germplasm introgression, genetic dissection, and genetic improvement of complex traits.
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association mapping of plant height yield and yield stability in recombinant Chromosome Substitution lines rcsls using hordeum vulgare subsp spontaneum as a source of donor alleles in a hordeum vulgare subsp vulgare background
Molecular Breeding, 2009Co-Authors: Luis Inostroza, Ivan Matus, Patrick M Hayes, Alejandro Del Pozo, Dalma Castillo, Stephen Machado, Ann CoreyAbstract:Grain yield and plant height of 80 recombinant Chromosome Substitution lines (RCSLs) of barley were measured in six environments with contrasting available moisture profiles. Two environments were in OR, USA (Moro and Pendleton) during one growing season (2004), and four in Chile (Cauquenes and Santa Rosa) during two growing seasons (2004/2005 and 2007/2008). From the yield data obtained in the different environments, yield adaptability (Finlay–Wilkinson slope) and stability (deviations from regression) were calculated. Two commercial cultivars (Harrington and Baronesse) were used as checks in all environments. Marker-quantitative trait associations were identified using 47 simple sequence repeats (SSRs) and the general linear model (GLM) implemented in TASSEL. The mean plant height and grain yield of the 80 RCSLs differed greatly across environments, reflecting differences in water availability. In all environments, there were significant differences (P < 0.05) in grain yield among RCSLs. There was also abundant variation in yield adaptability, indicating a differential response of the RCSLs to environmental conditions across environments. Using principal component analysis, it was possible to identify genotypes with better agronomic performance than the recurrent parent cv. Harrington. The association analysis revealed 21 chromosomal regions that were highly correlated with differences in grain yield, plant height and/or yield adaptability (Finlay–Wilkinson slope). In approximately one-fourth of the cases, the H. spontaneum donor contributed favorable alleles. The associations were referenced to the quantitative trait loci (QTL) for the same traits reported in the literature.
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Association mapping of plant height, yield, and yield stability in recombinant Chromosome Substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background
Molecular Breeding, 2009Co-Authors: Luis Inostroza, Ivan Matus, Alejandro Del Pozo, Dalma Castillo, Patrick Hayes, Stephen Machado, Ann CoreyAbstract:Grain yield and plant height of 80 recombinant Chromosome Substitution lines (RCSLs) of barley were measured in six environments with contrasting available moisture profiles. Two environments were in OR, USA (Moro and Pendleton) during one growing season (2004), and four in Chile (Cauquenes and Santa Rosa) during two growing seasons (2004/2005 and 2007/2008). From the yield data obtained in the different environments, yield adaptability (Finlay–Wilkinson slope) and stability (deviations from regression) were calculated. Two commercial cultivars (Harrington and Baronesse) were used as checks in all environments. Marker-quantitative trait associations were identified using 47 simple sequence repeats (SSRs) and the general linear model (GLM) implemented in TASSEL. The mean plant height and grain yield of the 80 RCSLs differed greatly across environments, reflecting differences in water availability. In all environments, there were significant differences ( P
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development and characterization of recombinant Chromosome Substitution lines rcsls using hordeum vulgare subsp spontaneum as a source of donor alleles in a hordeum vulgare subsp vulgare background
Genome, 2003Co-Authors: Ivan Matus, Kazuhiro Sato, Ann Corey, Tanya Filichkin, Patrick M Hayes, M I Vales, J G Kling, Oscar Rieralizarazu, W Powell, Robbie WaughAbstract:The ancestor of barley (Hordeum vulgare subsp. spontaneum) may be a source of novel alleles for crop improvement. We developed a set of recombinant Chromosome Substitution lines (RCSLs) using an accession of H. vulgare subsp. spontaneum (Caesarea 26-24, from Israel) as the donor and Hordeum vulgare subsp. vulgare 'Harrington' (the North American malting quality standard) as the recurrent parent via two backcrosses to the recurrent parent, followed by six generations of selfing. Here we report (i) the genomic architecture of the RCSLs, as inferred by simple sequence repeat (SSR) markers, and (ii) the effects of H. vulgare subsp. spontaneum genome segment introgressions in terms of three classes of phenotypes: inflorescence yield components, malting quality traits, and domestication traits. Significant differences among the RCSLs were detected for all phenotypes measured. The phenotypic effects of the introgressions were assessed using association analysis, and these were referenced to quantitative trait lo...