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Tomonori Takashi - One of the best experts on this subject based on the ideXlab platform.
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construction of rice chromosome segment Substitution Lines harboring oryza barthii genome and evaluation of yield related traits
Breeding Science, 2017Co-Authors: Kanako Besshouehara, Motoyuki Ashikari, Tomoyuki Furuta, Rosalyn B Angelesshim, Kengo Masuda, Shuto Yamada, Tomonori TakashiAbstract:Rice (Oryza sativa L.) is one of the most important staple food in the world. To meet the increasing demand for food, a strategy for improving rice yield is needed. Alleles of wild relatives are useful because they confer adaptation to plants under diverse harsh environments and have the potential to improve rice. O. barthii is a wild rice species endemic to Africa and the known progenitor of the African cultivated rice, O. glaberrima. To explore the genetic potential of the O. barthii as a genetic resource, 40 chromosome segment Substitution Lines (CSSL) of O. barthii in the background of the elite japonica cultivar Koshihikari were developed and evaluated to identify QTLs associated with 10 traits related to flag leaf morphology, grain yield and other agronomic traits. More than 90% of the entire genome of the donor parent was represented in contiguous or overlapping chromosome segments in the CSSLs. Evaluation of the CSSLs for several agriculturally important traits identified candidate chromosome segments that harbors QTLs associated with yield and yield-related traits. These results suggest that alleles from O. barthii might be used as a novel genetic resource for improving the yield-related traits in cultivars of O. sativa.
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development of chromosome segment Substitution Lines harboring oryza nivara genomic segments in koshihikari and evaluation of yield related traits
Breeding Science, 2016Co-Authors: Tomoyuki Furuta, Motoyuki Ashikari, Kanako Uehara, Rosalyn B Angelesshim, Junghyun Shim, Keisuke Nagai, Tomonori TakashiAbstract:Chromosome segment Substitution Lines (CSSLs) are rich genetic resources that can be mined for novel, agriculturally useful loci or that can be used directly as materials for breeding. To date, a number of rice CSSLs have been developed by crossing rice cultivars with its wild relatives as a means to tap into the potential of wild alleles in rice improvement. Oryza nivara is a wild relative of rice that is thought to be a progenitor of O. sativa spp. indica. In the present study, 26 CSSLs that covers the entire genome of O. nivara as contiguous, overlapping segments in the genomic background of a japonica cultivar, O. sativa cv. Koshihikari were developed. Evaluation of the CSSLs for several agriculturally important traits identified candidate chromosome segments that harbors QTLs associated with yield and yield-related traits. The results of the study revealed the potential of O. nivara as a source of novel alleles that can be used to improve the existing japonica cultivar.
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development and evaluation of chromosome segment Substitution Lines cssls carrying chromosome segments derived from oryza rufipogon in the genetic background of oryza sativa l
Breeding Science, 2014Co-Authors: Tomoyuki Furuta, Motoyuki Ashikari, Kanako Uehara, Rosalyn B Angelesshim, Junghyun Shim, Tomonori TakashiAbstract:The wild relatives of rice (Oryza sativa L.) are useful sources of alleles that have evolved to adapt in diverse environments around the world. Oryza rufipogon, the known progenitor of the cultivated rice, harbors genes that have been lost in cultivated varieties through domestication or evolution. This makes O. rufipogon an ideal source of value-added traits that can be utilized to improve the existing rice cultivars. To explore the potential of the rice progenitor as a genetic resource for improving O. sativa, 33 chromosome segment Substitution Lines (CSSLs) of O. rufipogon (W0106) in the background of the elite japonica cultivar Koshihikari were developed and evaluated for several agronomic traits. Over 90% of the entire genome was introgressed from the donor parent into the CSSLs. A total of 99 putative QTLs were detected, of which 15 were identified as major effective QTLs that have significantly large effects on the traits examined. Among the 15 major effective QTLs, a QTL on chromosome 10 showed a remarkable positive effect on the number of grains per panicle. Comparison of the putative QTLs identified in this study and previous studies indicated a wide genetic diversity between O. rufipogon accessions.
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development and evaluation of oryza glaberrima steud chromosome segment Substitution Lines cssls in the background of o sativa l cv koshihikari
Breeding Science, 2010Co-Authors: Rosalyn Angeles Shim, Motoyuki Ashikari, Enrique R Angeles, Tomonori TakashiAbstract:Oryza sativa and O. glaberrima are the cultivated forms of rice in Asia and Africa, respectively. While both possess important agricultural traits, genes that are unique to either species can be used to improve the other. To explore the genetic potential of the African rice as a genetic resource for the improvement of O. sativa, 34 chromosome segment Substitution Lines of O. glaberrima in the background of the elite japonica cultivar Koshihikari were developed and used to identify QTLs associated with 10 traits related to grain yield, plant stature and maturity. More than 90% of the entire genome of the donor parent was represented in contiguous or overlapping chromosome segments in the CSSL set. A total of 105 putative QTLs were identified, 84 of which had positive and 21 had negative effects on the traits examined. Of the 84 QTLs with positive effects, 64 were associated with increase in grain length, grain width, grain thickness, 100-grain weight, grain number per panicle and number of primary branches per panicle whereas 20 QTLs control plant stature. These results suggest that alleles from the African rice may be useful in improving traits related to grain yield and plant stature in existing cultivars of O. sativa.
Kazuhiro Sato - One of the best experts on this subject based on the ideXlab platform.
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an application of high throughput snp genotyping for barley genome mapping and characterization of recombinant chromosome Substitution Lines
Theoretical and Applied Genetics, 2009Co-Authors: Kazuhiro Sato, Kazuyoshi TakedaAbstract:An oligo-nucleotide pooled assay (OPA) for high-throughput single nucleotide polymorphism (SNP) genotyping was used for genetic map development in order to coordinate marker information from multiple mapping resources in barley. A doubled haploid (DH) population derived from the cross between barley cultivar “Haruna Nijo” (Hordeum vulgare ssp. vulgare) and wild barley strain “H602” (H. vulgare ssp. spontaneum) was genotyped with 1,448 unigene-derived OPA-SNPs. Of these, 732 markers showed polymorphisms and 384 were cross-referenced with EST markers on our high-density transcript map. The OPA-SNP markers were well distributed on barley chromosomes as follows: 1H (93), 2H (131), 3H (123), 4H (97), 5H (108), 6H (92) and 7H (88). Using a cMAP platform, it was possible to integrate EST marker positions across high-density EST maps. The OPA-SNPs were used to genotype 99 BC3F5 recombinant chromosome Substitution Lines (RCSLs) from the same cross (Haruna Nijo/H602). These data were used to create graphical genotypes for each line and thus estimate the location, extent, and total number of introgressions from the wild barley parent. The RCSLs sampled most of the wild barley genome, with only a few missing segments. With the resources we have developed, all QTL alleles segregating in this germplasm are now potential targets for map-based cloning.
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qtl analysis in recombinant chromosome Substitution Lines and doubled haploid Lines derived from a cross between hordeum vulgare ssp vulgare and hordeum vulgare ssp spontaneum
Molecular Breeding, 2005Co-Authors: Kiyosumi Hori, Kazuhiro Sato, Nami Nankaku, Kazuyoshi TakedaAbstract:Recombinant chromosome Substitution Lines (RCSLs) were developed in BC3 generation to introduce segments of a wild barley strain ‘H602’ (Hordeum vulgare ssp. spontaneum) into a barley cultivar ‘Haruna Nijo’ (H. vulgare ssp. vulgare) genetic background. One hundred thirty four RCSLs were genotyped by 25 SSR and 60 EST markers, which were localized on a linkage map of doubled haploid Lines (DHLs) derived from the same cross combination. Graphical genotyping revealed that the observed average Substitution ratio of H602 segment (12.9%) agreed with the expected Substitution ratio (12.5%), and a minimum set of 19 RCSLs represented the entire H602 genome. Phenotypes of five qualitative and nine quantitative traits were scored in both the RCSLs and DHLs. Five qualitative traits were localized as morphological markers on the linkage map of the DHLs, and these molecular markers were aligned on the respective chromosomal regions in the RCSLs. Simple and composite interval mapping procedures detected a total of 18 and 24 QTLs for nine qualitative traits on the RCSLs and DHLs, respectively. Several QTLs were localized at coincident or very close regions on both linkage maps. In spite of general inferior agronomic performances in wild barley, several H602 QTL alleles showed agronomically positive effects. These RCSLs should contribute to Substitution of favorable alleles from wild barley into cultivated barley. These RCSLs are also available as sources of near isogenic Lines, with which we can apply advanced genetic analysis methods such as isolation of QTLs and detection of epistatic interactions among QTLs.
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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...
Kazuyoshi Takeda - One of the best experts on this subject based on the ideXlab platform.
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an application of high throughput snp genotyping for barley genome mapping and characterization of recombinant chromosome Substitution Lines
Theoretical and Applied Genetics, 2009Co-Authors: Kazuhiro Sato, Kazuyoshi TakedaAbstract:An oligo-nucleotide pooled assay (OPA) for high-throughput single nucleotide polymorphism (SNP) genotyping was used for genetic map development in order to coordinate marker information from multiple mapping resources in barley. A doubled haploid (DH) population derived from the cross between barley cultivar “Haruna Nijo” (Hordeum vulgare ssp. vulgare) and wild barley strain “H602” (H. vulgare ssp. spontaneum) was genotyped with 1,448 unigene-derived OPA-SNPs. Of these, 732 markers showed polymorphisms and 384 were cross-referenced with EST markers on our high-density transcript map. The OPA-SNP markers were well distributed on barley chromosomes as follows: 1H (93), 2H (131), 3H (123), 4H (97), 5H (108), 6H (92) and 7H (88). Using a cMAP platform, it was possible to integrate EST marker positions across high-density EST maps. The OPA-SNPs were used to genotype 99 BC3F5 recombinant chromosome Substitution Lines (RCSLs) from the same cross (Haruna Nijo/H602). These data were used to create graphical genotypes for each line and thus estimate the location, extent, and total number of introgressions from the wild barley parent. The RCSLs sampled most of the wild barley genome, with only a few missing segments. With the resources we have developed, all QTL alleles segregating in this germplasm are now potential targets for map-based cloning.
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qtl analysis in recombinant chromosome Substitution Lines and doubled haploid Lines derived from a cross between hordeum vulgare ssp vulgare and hordeum vulgare ssp spontaneum
Molecular Breeding, 2005Co-Authors: Kiyosumi Hori, Kazuhiro Sato, Nami Nankaku, Kazuyoshi TakedaAbstract:Recombinant chromosome Substitution Lines (RCSLs) were developed in BC3 generation to introduce segments of a wild barley strain ‘H602’ (Hordeum vulgare ssp. spontaneum) into a barley cultivar ‘Haruna Nijo’ (H. vulgare ssp. vulgare) genetic background. One hundred thirty four RCSLs were genotyped by 25 SSR and 60 EST markers, which were localized on a linkage map of doubled haploid Lines (DHLs) derived from the same cross combination. Graphical genotyping revealed that the observed average Substitution ratio of H602 segment (12.9%) agreed with the expected Substitution ratio (12.5%), and a minimum set of 19 RCSLs represented the entire H602 genome. Phenotypes of five qualitative and nine quantitative traits were scored in both the RCSLs and DHLs. Five qualitative traits were localized as morphological markers on the linkage map of the DHLs, and these molecular markers were aligned on the respective chromosomal regions in the RCSLs. Simple and composite interval mapping procedures detected a total of 18 and 24 QTLs for nine qualitative traits on the RCSLs and DHLs, respectively. Several QTLs were localized at coincident or very close regions on both linkage maps. In spite of general inferior agronomic performances in wild barley, several H602 QTL alleles showed agronomically positive effects. These RCSLs should contribute to Substitution of favorable alleles from wild barley into cultivated barley. These RCSLs are also available as sources of near isogenic Lines, with which we can apply advanced genetic analysis methods such as isolation of QTLs and detection of epistatic interactions among QTLs.
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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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...
Masahiro Yano - One of the best experts on this subject based on the ideXlab platform.
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genetic mechanisms underlying yield potential in the rice high yielding cultivar takanari based on reciprocal chromosome segment Substitution Lines
BMC Plant Biology, 2014Co-Authors: Toshiyuki Takai, Masahiro Yano, Yasunori Nonoue, Nozomi Ono, Takashi Ikka, Katsuhiko Kondo, Yumiko Araisanoh, Satoshi Yoshinaga, Hiroshi Nakano, Motohiko KondoAbstract:Increasing rice yield potential is a major objective in rice breeding programs, given the need for meeting the demands of population growth, especially in Asia. Genetic analysis using genomic information and high-yielding cultivars can facilitate understanding of the genetic mechanisms underlying rice yield potential. Chromosome segment Substitution Lines (CSSLs) are a powerful tool for the detection and precise mapping of quantitative trait loci (QTLs) that have both large and small effects. In addition, reciprocal CSSLs developed in both parental cultivar backgrounds may be appropriate for evaluating gene activity, as a single factor or in epistatic interactions. We developed reciprocal CSSLs derived from a cross between Takanari (one of the most productive indica cultivars) and a leading japonica cultivar, Koshihikari; both the cultivars were developed in Japan. Forty-one CSSLs covered most of the Takanari genome in the Koshihikari background and 39 CSSLs covered the Koshihikari genome in the Takanari background. Using the reciprocal CSSLs, we conducted yield trials under canopy conditions in paddy fields. While no CSSLs significantly exceeded the recurrent parent cultivar in yield, genetic analysis detected 48 and 47 QTLs for yield and its components in the Koshihikari and Takanari backgrounds, respectively. A number of QTLs showed a trade-off, in which the allele with increased sink-size traits (spikelet number per panicle or per square meter) was associated with decreased ripening percentage or 1000-grain weight. These results indicate that increased sink size is not sufficient to increase rice yield in both backgrounds. In addition, most QTLs were detected in either one of the two genetic backgrounds, suggesting that these loci may be under epistatic control with other gene(s). We demonstrated that the reciprocal CSSLs are a useful tool for understanding the genetic mechanisms underlying yield potential in the high-yielding rice cultivar Takanari. Our results suggest that sink-size QTLs in combination with QTLs for source strength or translocation capacity, as well as careful attention to epistatic interactions, are necessary for increasing rice yield. Thus, our findings provide a foundation for developing rice cultivars with higher yield potential in future breeding programs.
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detection of qtls to reduce cadmium content in rice grains using lac23 koshihikari chromosome segment Substitution Lines
Breeding Science, 2013Co-Authors: Tadashi Abe, Toshio Yamamoto, Shuichi Fukuoka, Masahiro Yano, Yasunori Nonoue, Nozomi Ono, Motoyasu Omoteno, Masato Kuramata, Satoru IshikawaAbstract:To advance the identification of quantitative trait loci (QTLs) to reduce Cd content in rice (Oryza sativa L.) grains and breed low-Cd cultivars, we developed a novel population consisting of 46 chromosome segment Substitution Lines (CSSLs) in which donor segments of LAC23, a cultivar reported to have a low grain Cd content, were substituted into the Koshihikari genetic background. The parental cultivars and 32 CSSLs (the minimum set required for whole-genome coverage) were grown in two fields with different natural levels of soil Cd. QTL mapping by single-marker analysis using ANOVA indicated that eight chromosomal regions were associated with grain Cd content and detected a major QTL (qlGCd3) with a high F-test value in both fields (F = 9.19 and 5.60) on the long arm of chromosome 3. The LAC23 allele at qlGCd3 was associated with reduced grain Cd levels and appeared to reduce Cd transport from the shoots to the grains. Fine Substitution mapping delimited qlGCd3 to a 3.5-Mbp region. Our results suggest that the low-Cd trait of LAC23 is controlled by multiple QTLs, and qlGCd3 is a promising candidate QTL to reduce the Cd level of rice grain.
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mapping and characterization of seed dormancy qtls using chromosome segment Substitution Lines in rice
Theoretical and Applied Genetics, 2012Co-Authors: Salem Marzougui, Kiyosumi Hori, Kazuhiko Sugimoto, Utako Yamanouchi, Masaki Shimono, Tomoki Hoshino, Masatomo Kobayashi, Kanako Ishiyama, Masahiro YanoAbstract:Seed dormancy—the temporary failure of a viable seed to germinate under favorable conditions—is a complex characteristic influenced by many genes and environmental factors. To detect the genetic factors associated with seed dormancy in rice, we conducted a QTL analysis using chromosome segment Substitution Lines (CSSLs) derived from a cross between Nona Bokra (strong dormancy) and Koshihikari (weak dormancy). Comparison of the levels of seed dormancy of the CSSLs and their recurrent parent Koshihikari revealed that two chromosomal regions—on the short arms of chromosomes 1 and 6—were involved in the variation in seed dormancy. Further genetic analyses using an F2 population derived from crosses between the CSSLs and Koshihikari confirmed the allelic differences and the chromosomal locations of three putative QTLs: Sdr6 on chromosome 1 and Sdr9 and Sdr10 on chromosome 6. The Nona Bokra alleles of the three QTLs were associated with decreased germination rate. We discuss the physiological features of the CSSLs and speculate on the possible mechanisms of dormancy in light of the newly detected QTLs.
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detection of quantitative trait loci controlling pre harvest sprouting resistance by using backcrossed populations of japonica rice cultivars
Theoretical and Applied Genetics, 2010Co-Authors: Kiyosumi Hori, Kazuhiko Sugimoto, Utako Yamanouchi, Yoshinobu Takeuchi, Yasunori Nonoue, Nozomi Ono, Kazuki Matsubara, Akira Abe, Masahiro YanoAbstract:Backcrossed inbred Lines (BILs) and a set of reciprocal chromosome segment Substitution Lines (CSSLs) derived from crosses between japonica rice cultivars Nipponbare and Koshihikari were used to detect quantitative trait loci (QTLs) for pre-harvest sprouting resistance. In the BILs, we detected one QTL on chromosome 3 and one QTL on chromosome 12. The QTL on the short arm of chromosome 3 accounted for 45.0% of the phenotypic variance and the Nipponbare allele of the QTL increased germination percentage by 21.3%. In the CSSLs, we detected seven QTLs, which were located on chromosomes 2, 3 (two), 5, 8 and 11 (two). All Nipponbare alleles of the QTLs were associated with an increased rate of germination. The major QTL for pre-harvest sprouting resistance on the short arm of chromosome 3 was localized to a 474-kbp region in the Nipponbare genome by the SSR markers RM14240 and RM14275 by using 11 Substitution Lines to replace the different short chromosome segments on chromosome 3. This QTL co-localized with the low-temperature germinability gene qLTG3-1. The level of germinability under low temperature strongly correlated with the level of pre-harvest sprouting resistance in the Substitution Lines. Sequence analyses revealed a novel functional allele of qLTG3-1 in Nipponbare and a loss-of-function allele in Koshihikari. The allelic difference in qLTG3-1 between Nipponbare and Koshihikari is likely to be associated with differences in both pre-harvest sprouting resistance and low-temperature germinability.
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genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment Substitution Lines in rice
Theoretical and Applied Genetics, 2008Co-Authors: Tsuyu Ando, Toshio Yamamoto, Takehiko Shimizu, Xiu Fang, Ayahiko Shomura, Yoshinobu Takeuchi, Shaoyang Lin, Masahiro YanoAbstract:To understand the genetic basis of yield-related traits of rice, we developed 39 chromosome segment Substitution Lines (CSSLs) from a cross between an average-yielding japonica cultivar, Sasanishiki, as the recurrent parent and a high-yielding indica cultivar, Habataki, as the donor. Five morphological components of panicle architecture in the CSSLs were evaluated in 2 years, and 38 quantitative trait loci (QTLs) distributed on 11 chromosomes were detected. The additive effect of each QTL was relatively small, suggesting that none of the QTLs could explain much of the phenotypic difference in sink size between Sasanishiki and Habataki. We developed nearly isogenic Lines for two major QTLs, qSBN1 (for secondary branch number on chromosome 1) and qPBN6 (for primary branch number on chromosome 6), and a line containing both. Phenotypic analysis of these Lines revealed that qSBN1 and qPBN6 contributed independently to sink size and that the combined line produced more spikelets. This suggests that the cumulative effects of QTLs distributed throughout the genome form the major genetic basis of panicle architecture in rice.
