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Yanrong Wang - One of the best experts on this subject based on the ideXlab platform.
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Construction of the first high-density genetic linkage map and identification of Seed yield-related QTLs and candidate genes in Elymus sibiricus, an important forage grass in Qinghai-Tibet Plateau
BMC Genomics, 2019Co-Authors: Zongyu Zhang, Junchao Zhang, Yongqiang Zhao, Na Wang, Yanrong WangAbstract:Elymus sibiricus is an ecologically and economically important perennial, self-pollinated, and allotetraploid (StStHH) grass, widely used for forage production and animal husbandry in Western and Northern China. However, it has low Seed yield mainly caused by Seed Shattering, which makes Seed production difficult for this species. The goals of this study were to construct the high-density genetic linkage map, and to identify QTLs and candidate genes for Seed-yield related traits. An F2 mapping population of 200 individuals was developed from a cross between single genotype from “Y1005” and “ZhN06”. Specific-locus amplified fragment sequencing (SLAF-seq) was applied to construct the first genetic linkage map. The final genetic map included 1971 markers on the 14 linkage groups (LGs) and was 1866.35 cM in total. The length of each linkage group varied from 87.67 cM (LG7) to 183.45 cM (LG1), with an average distance of 1.66 cM between adjacent markers. The marker sequences of E. sibiricus were compared to two grass genomes and showed 1556 (79%) markers mapped to wheat, 1380 (70%) to barley. Phenotypic data of eight Seed-related traits (2016–2018) were used for QTL identification. A total of 29 QTLs were detected for eight Seed-related traits on 14 linkage groups, of which 16 QTLs could be consistently detected for two or three years. A total of 6 QTLs were associated with Seed Shattering. Based on annotation with wheat and barley genome and transcriptome data of abscission zone in E. sibiricus, we identified 30 candidate genes for Seed Shattering, of which 15, 7, 6 and 2 genes were involved in plant hormone signal transcription, transcription factor, hydrolase activity and lignin biosynthetic pathway, respectively. This study constructed the first high-density genetic linkage map and identified QTLs and candidate genes for Seed-related traits in E. sibiricus. Results of this study will not only serve as genome-wide resources for gene/QTL fine mapping, but also provide a genetic framework for anchoring sequence scaffolds on chromosomes in future genome sequence assembly of E. sibiricus.
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Hybrid identification and genetic variation of Elymus sibiricus hybrid populations using EST-SSR markers.
Hereditas, 2017Co-Authors: Xuhong Zhao, Junchao Zhang, Zongyu Zhang, Yanrong WangAbstract:Elymus sibiricus is an important native grass in Qinghai-Tibetan Plateau. Seed Shattering is a serious problem for E. sibiricus, especially at harvest time. Cross breeding is an effective way to create new varieties with beneficial characteristic or improved traits, and to broaden genetic base. In this study, we created five hybrid populations by crossing seven E. sibiricus genotypes that have Seed Shattering variation. Then, nine EST-SSR primers were used for hybrid identification based on DNA fingerprinting, and genetic diversity analysis of hybrid populations and their respective parents. A total of 15 hybrids were identified. An analysis of amplified polymorphic bands among genuine hybrids and their respective parents revealed mainly two types of markers: 1) hybrids shared bands exclusively amplified in both parents; 2)hybrids shared bands exclusively amplified in male parents. For each hybrid population, the total number of amplified bands ranged from 37 to 57, the percentage of polymorphism varied from 65.12% to 75.68%, with an average of 70.51%. Novel bands found in each hybrid population varied from 0 to 9 bands, suggesting an occurrence of rearrangements in the hybrid population. The structure analysis revealed that all hybrid populations and parents were assigned to eight groups. The principal coordinate analysis (PCoA) showed similar results. In general, this study proved EST-SSR markers are efficient for hybrid identification, and suggested more genetic variation could be captured in hybrid populations by crossing breeding.
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transcriptome profiling of elymus sibiricus an important forage grass in qinghai tibet plateau reveals novel insights into candidate genes that potentially connected to Seed Shattering
BMC Plant Biology, 2017Co-Authors: Junchao Zhang, Xuhong Zhao, Zongyu Zhang, Yanrong WangAbstract:Elymus sibiricus is an important forage grass in semi-arid regions, but it is difficult to grow for commercial Seed production due to high Seed Shattering. To better understand the underlying mechanism and explore the putative genes related to Seed Shattering, we conducted a combination of morphological, histological, physiochemical and transcriptome analysis on two E. sibiricus genotypes (XH09 and ZhN03) that have contrasting Seed Shattering. The results show that Seed Shattering is generally caused by a degradation of the abscission layer. Early degradation of abscission layers was associated with the increased Seed Shattering in high Seed Shattering genotype XH09. Two cell wall degrading enzymes, cellulase (CE) and polygalacturonase (PG), had different activity in the abscission zone, indicating their roles in differentiation of abscission layer. cDNA libraries from abscission zone tissue of XH09 and ZhN03 at 7 days, 21 days and 28 days after heading were constructed and sequenced. A total of 86,634 unigenes were annotated and 7110 differentially expressed transcripts (DETs) were predicted from “XH09-7 vs ZhN03-7”, “XH09-21 vs ZhN03-21” and “XH09-28 vs ZhN03-28”, corresponding to 2058 up-regulated and 5052 down-regulated unigenes. The expression profiles of 10 candidate transcripts involved in cell wall-degrading enzymes, lignin biosynthesis and phytohormone activity were validated using quantitative real-time PCR (qRT-PCR), 8 of which were up-regulated in low Seed Shattering genotype ZhN03, suggesting these genes may be associated with reduction of Seed Shattering. The expression data generated in this study provides an important resource for future molecular biological research in E. sibiricus.
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histological characteristics cell wall hydrolytic enzymes activity and candidate genes expression associated with Seed Shattering of elymus sibiricus accessions
Frontiers in Plant Science, 2017Co-Authors: Xuhong Zhao, Junchao Zhang, Zongyu Zhang, Yanrong WangAbstract:Elymus sibiricus (siberian wildrye) is a perennial, cool-season, self-pollinating, and allotetraploid grass. As an economically important species, it has been widely grown and used for pasture and hay in northern China. Because of serious Seed Shattering, however, E. sibiricus is difficult to grow for commercial Seed production. To better understand the underlying mechanism of Seed Shattering, we investigated the differences in Seed Shattering of cultivars and wild accessions in relation to morphological and genetic diversity, histological characteristics, lignin staining, cell wall hydrolytic enzymes activity and candidate genes expressions. We found high level of morphological and genetic diversity among E. sibiricus accessions. In general, cultivars had higher average pedicel breaking tensile strength (BTS) value than wild accessions, of which PI655199 had the highest average BTS value (144.51 gf) and LQ04 had the lowest average BTS value (47.17 gf) during Seed development. Seed Shattering showed a significant correlation with Seed length (SL), awn length (AL) and 1000-Seed weight (KW). Seed Shattering was caused by degradation of abscission layers that formed at early heading stage, and degradation of abscission layers occurred at 14 days after heading (DAH). Histological analysis of abscission zone showed a smooth fracture surface on the rachilla in high Seed Shattering genotype, suggesting higher degradation degree of abscission layers. This may resulted from the increased cellulase (CE) and polygalacturonase (PG) activity found in abscission zone at Seed physiological maturity. Staining of pedicels of two contrasting genotypes suggested more lignin deposition in low Seed Shattering genotype may play an role in resistance of Seed Shattering. Furthermore, candidate genes that involved in cell wall-degrading enzyme and lignin biosynthesis were differentially expressed in abscission zone, indicating the involvement and role in Seed Shattering. This study provided novel insights into the mechanism of Seed Shattering in E. sibiricus.
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assessing and broadening genetic diversity of elymus sibiricus germplasm for the improvement of Seed Shattering
Molecules, 2016Co-Authors: Zongyu Zhang, Xuhong Zhao, Junchao Zhang, Yanrong WangAbstract:Siberian wild rye (Elymus sibiricus L.) is an important native grass in the Qinghai-Tibet Plateau of China. It is difficult to grow for commercial Seed production, since Seed Shattering causes yield losses during harvest. Assessing the genetic diversity and relationships among germplasm from its primary distribution area contributes to evaluating the potential for its utilization as a gene pool to improve the desired agronomic traits. In the study, 40 EST-SSR primers were used to assess the genetic diversity and population structure of 36 E. sibiricus accessions with variation of Seed Shattering. A total of 380 bands were generated, with an average of 9.5 bands per primer. The polymorphic information content (PIC) ranged from 0.23 to 0.50. The percentage of polymorphic bands (P) for the species was 87.11%, suggesting a high degree of genetic diversity. Based on population structure analysis, four groups were formed, similar to results of principal coordinate analysis (PCoA). The molecular variance analysis (AMOVA) revealed the majority of genetic variation occurred within geographical regions (83.40%). Two genotypes from Y1005 and ZhN06 were used to generate seven F1 hybrids. The molecular and morphological diversity analysis of F1 population revealed rich genetic variation and high level of Seed Shattering variation in F1 population, resulting in significant improvement of the genetic base and desired agronomic traits.
Bao-rong Lu - One of the best experts on this subject based on the ideXlab platform.
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reduced weed Seed Shattering by silencing a cultivated rice gene strategic mitigation for escaped transgenes
Transgenic Research, 2017Co-Authors: Lei Li, Lei Wang, Xiaoqi Jiang, Jia Fang, Feng Wang, Jun Su, Bao-rong LuAbstract:Transgene flow form a genetically engineered (GE) crop to its wild relatives may result in unwanted environmental consequences. Mitigating transgenes via introducing a gene that is disadvantageous to wild relatives but beneficial to crops, and is tightly-linked with the target transgenes, may provide a promising solution to limit the spread of transgenes in wild/weedy populations. Here we demonstrate a novel system with significantly reduced Seed Shattering in crop-weed hybrid descendants by partially silenced expression of the Seed-Shattering gene SH4 in cultivated rice, using artificial microRNA and antisense RNA techniques. Accordingly, fewer Seeds were found in the soil of the field plots where transgenic hybrid lineages were grown. However, no differences in productivity-related traits were detected between GE and non-GE cultivated rice. To silence Seed-Shattering genes provides a useful strategy to reduce the potential environmental impacts caused by transgene flow from commercial GE rice to weedy rice, in addition to the control of weedy rice.
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multiple tissue specific expression of rice Seed Shattering gene sh4 regulated by its promoter psh4
Rice, 2015Co-Authors: L I, Jun Su, Zhe Wang, Bao-rong LuAbstract:Background Rice Seed Shattering is an important domestication syndrome encoded by a gene named as SH4. The coding region of SH4 has been well studied regarding its function and roles in evolution. However, its promoter has not been identified, which limited our understanding of the detailed regulatory mechanisms of this gene. It is therefore critical to characterize the promoter and study its expression pattern.
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mapping quantitative trait loci qtl determining Seed Shattering in weedy rice evolution of Seed Shattering in weedy rice through de domestication
Euphytica, 2015Co-Authors: Lei Wang, Bao-rong LuAbstract:Seed Shattering is an important trait that distinguishes domesticated plants from their wild and weedy counterparts. This trait is essential for Seed harvesting in the production of cereal crops, and therefore has attracted great attention of scientists to study the underlying genetic mechanisms of Seed persistence/Shattering during crop domestication. To study Seed Shattering in weedy rice, we analyzed the F2 offspring derived from artificial crosses between a non-Shattering rice variety Minghui86 and a weedy rice accession WD1292 with strong Seed Shattering. We identified three Seed-Shattering associated quantitative trait loci (QTL), wd-qsh1, wd-qsh3, and wd-qsh5 located on chromosome-1, -3 and -5, respectively, based on the microsatellite (SSR) variation pattern of the crop-weed F2 offspring. The wd-qsh3 had the greatest contribution to Seed Shattering by explaining 31.41 % of the phenotypic variance, and the two remaining QTLs had relatively minor effects on phenotypic variation, ranging from 11.61 to 16.85 %. Comparative analysis indicated that the mapped QTLs (wd-qsh1, wd-qsh3 and wd-qsh5) from this study had no overlaps with any of the previously reported major Shattering loci (e.g., SH4, qSH1, sh-h, and SHAT1) identified using a diverse set of rice germplasm, including cultivated, wild, and weedy rice lines. These results suggest that distinct genetic mechanisms should be evolved independently in different weedy rice groups, which allows weedy rice to adapt to the diverse agricultural environments. De-domestication plays a significant role in generating weedy rice without the involvement of wild rice in agro-ecosystems.
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sequence polymorphisms in wild weedy and cultivated rice suggest Seed Shattering locus sh4 played a minor role in asian rice domestication
Ecology and Evolution, 2012Co-Authors: Yongqing Zhu, Norman C Ellstrand, Bao-rong LuAbstract:The predominant view regarding Asian rice domestication is that the initial origin of nonShattering involved a single gene of large effect, specifically, the sh4 locus via the evolutionary replacement of a dominant allele for Shattering with a recessive allele for reduced Shattering. Data have accumulated to challenge this hypothesis. Specifically, a few studies have reported occasional Seed-Shattering plants from populations of the wild progenitor of cultivated rice (Oryza rufipogon complex) being homozygous for the putative “nonShattering” sh4 alleles. We tested the sh4 hypothesis for the domestication of cultivated rice by obtaining genotypes and phenotypes for a diverse set of samples of wild, weedy, and cultivated rice accessions. The cultivars were fixed for the putative “nonShattering” allele and nonShattering phenotype, but wild rice accessions are highly polymorphic for the putative “nonShattering” allele (frequency ~26%) with Shattering phenotype. All weedy rice accessions are the “nonShattering” genotype at the sh4 locus but with Shattering phenotype. These data challenge the widely accepted hypothesis that a single nucleotide mutation (“G”/“T”) of the sh4 locus is the major driving force for rice domestication. Instead, we hypothesize that unidentified Shattering loci are responsible for the initial domestication of cultivated rice through reduced Seed Shattering.
Zongyu Zhang - One of the best experts on this subject based on the ideXlab platform.
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Construction of the first high-density genetic linkage map and identification of Seed yield-related QTLs and candidate genes in Elymus sibiricus, an important forage grass in Qinghai-Tibet Plateau
BMC Genomics, 2019Co-Authors: Zongyu Zhang, Junchao Zhang, Yongqiang Zhao, Na Wang, Yanrong WangAbstract:Elymus sibiricus is an ecologically and economically important perennial, self-pollinated, and allotetraploid (StStHH) grass, widely used for forage production and animal husbandry in Western and Northern China. However, it has low Seed yield mainly caused by Seed Shattering, which makes Seed production difficult for this species. The goals of this study were to construct the high-density genetic linkage map, and to identify QTLs and candidate genes for Seed-yield related traits. An F2 mapping population of 200 individuals was developed from a cross between single genotype from “Y1005” and “ZhN06”. Specific-locus amplified fragment sequencing (SLAF-seq) was applied to construct the first genetic linkage map. The final genetic map included 1971 markers on the 14 linkage groups (LGs) and was 1866.35 cM in total. The length of each linkage group varied from 87.67 cM (LG7) to 183.45 cM (LG1), with an average distance of 1.66 cM between adjacent markers. The marker sequences of E. sibiricus were compared to two grass genomes and showed 1556 (79%) markers mapped to wheat, 1380 (70%) to barley. Phenotypic data of eight Seed-related traits (2016–2018) were used for QTL identification. A total of 29 QTLs were detected for eight Seed-related traits on 14 linkage groups, of which 16 QTLs could be consistently detected for two or three years. A total of 6 QTLs were associated with Seed Shattering. Based on annotation with wheat and barley genome and transcriptome data of abscission zone in E. sibiricus, we identified 30 candidate genes for Seed Shattering, of which 15, 7, 6 and 2 genes were involved in plant hormone signal transcription, transcription factor, hydrolase activity and lignin biosynthetic pathway, respectively. This study constructed the first high-density genetic linkage map and identified QTLs and candidate genes for Seed-related traits in E. sibiricus. Results of this study will not only serve as genome-wide resources for gene/QTL fine mapping, but also provide a genetic framework for anchoring sequence scaffolds on chromosomes in future genome sequence assembly of E. sibiricus.
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elymus nutans genes for Seed Shattering and candidate gene derived est ssr markers for germplasm evaluation
BMC Plant Biology, 2019Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu ZhangAbstract:Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial Seed production due to serious Seed Shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with Seed Shattering, explore candidate genes involved in Seed Shattering and identify candidate gene-based EST-SSR markers for germplasm evaluation. cDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and Seed Shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting Seed Shattering habit. The dendrogram based on molecular data showed that most accessions with similar Seed Shattering degree tended to group together. The expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future.
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Hybrid identification and genetic variation of Elymus sibiricus hybrid populations using EST-SSR markers.
Hereditas, 2017Co-Authors: Xuhong Zhao, Junchao Zhang, Zongyu Zhang, Yanrong WangAbstract:Elymus sibiricus is an important native grass in Qinghai-Tibetan Plateau. Seed Shattering is a serious problem for E. sibiricus, especially at harvest time. Cross breeding is an effective way to create new varieties with beneficial characteristic or improved traits, and to broaden genetic base. In this study, we created five hybrid populations by crossing seven E. sibiricus genotypes that have Seed Shattering variation. Then, nine EST-SSR primers were used for hybrid identification based on DNA fingerprinting, and genetic diversity analysis of hybrid populations and their respective parents. A total of 15 hybrids were identified. An analysis of amplified polymorphic bands among genuine hybrids and their respective parents revealed mainly two types of markers: 1) hybrids shared bands exclusively amplified in both parents; 2)hybrids shared bands exclusively amplified in male parents. For each hybrid population, the total number of amplified bands ranged from 37 to 57, the percentage of polymorphism varied from 65.12% to 75.68%, with an average of 70.51%. Novel bands found in each hybrid population varied from 0 to 9 bands, suggesting an occurrence of rearrangements in the hybrid population. The structure analysis revealed that all hybrid populations and parents were assigned to eight groups. The principal coordinate analysis (PCoA) showed similar results. In general, this study proved EST-SSR markers are efficient for hybrid identification, and suggested more genetic variation could be captured in hybrid populations by crossing breeding.
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transcriptome profiling of elymus sibiricus an important forage grass in qinghai tibet plateau reveals novel insights into candidate genes that potentially connected to Seed Shattering
BMC Plant Biology, 2017Co-Authors: Junchao Zhang, Xuhong Zhao, Zongyu Zhang, Yanrong WangAbstract:Elymus sibiricus is an important forage grass in semi-arid regions, but it is difficult to grow for commercial Seed production due to high Seed Shattering. To better understand the underlying mechanism and explore the putative genes related to Seed Shattering, we conducted a combination of morphological, histological, physiochemical and transcriptome analysis on two E. sibiricus genotypes (XH09 and ZhN03) that have contrasting Seed Shattering. The results show that Seed Shattering is generally caused by a degradation of the abscission layer. Early degradation of abscission layers was associated with the increased Seed Shattering in high Seed Shattering genotype XH09. Two cell wall degrading enzymes, cellulase (CE) and polygalacturonase (PG), had different activity in the abscission zone, indicating their roles in differentiation of abscission layer. cDNA libraries from abscission zone tissue of XH09 and ZhN03 at 7 days, 21 days and 28 days after heading were constructed and sequenced. A total of 86,634 unigenes were annotated and 7110 differentially expressed transcripts (DETs) were predicted from “XH09-7 vs ZhN03-7”, “XH09-21 vs ZhN03-21” and “XH09-28 vs ZhN03-28”, corresponding to 2058 up-regulated and 5052 down-regulated unigenes. The expression profiles of 10 candidate transcripts involved in cell wall-degrading enzymes, lignin biosynthesis and phytohormone activity were validated using quantitative real-time PCR (qRT-PCR), 8 of which were up-regulated in low Seed Shattering genotype ZhN03, suggesting these genes may be associated with reduction of Seed Shattering. The expression data generated in this study provides an important resource for future molecular biological research in E. sibiricus.
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histological characteristics cell wall hydrolytic enzymes activity and candidate genes expression associated with Seed Shattering of elymus sibiricus accessions
Frontiers in Plant Science, 2017Co-Authors: Xuhong Zhao, Junchao Zhang, Zongyu Zhang, Yanrong WangAbstract:Elymus sibiricus (siberian wildrye) is a perennial, cool-season, self-pollinating, and allotetraploid grass. As an economically important species, it has been widely grown and used for pasture and hay in northern China. Because of serious Seed Shattering, however, E. sibiricus is difficult to grow for commercial Seed production. To better understand the underlying mechanism of Seed Shattering, we investigated the differences in Seed Shattering of cultivars and wild accessions in relation to morphological and genetic diversity, histological characteristics, lignin staining, cell wall hydrolytic enzymes activity and candidate genes expressions. We found high level of morphological and genetic diversity among E. sibiricus accessions. In general, cultivars had higher average pedicel breaking tensile strength (BTS) value than wild accessions, of which PI655199 had the highest average BTS value (144.51 gf) and LQ04 had the lowest average BTS value (47.17 gf) during Seed development. Seed Shattering showed a significant correlation with Seed length (SL), awn length (AL) and 1000-Seed weight (KW). Seed Shattering was caused by degradation of abscission layers that formed at early heading stage, and degradation of abscission layers occurred at 14 days after heading (DAH). Histological analysis of abscission zone showed a smooth fracture surface on the rachilla in high Seed Shattering genotype, suggesting higher degradation degree of abscission layers. This may resulted from the increased cellulase (CE) and polygalacturonase (PG) activity found in abscission zone at Seed physiological maturity. Staining of pedicels of two contrasting genotypes suggested more lignin deposition in low Seed Shattering genotype may play an role in resistance of Seed Shattering. Furthermore, candidate genes that involved in cell wall-degrading enzyme and lignin biosynthesis were differentially expressed in abscission zone, indicating the involvement and role in Seed Shattering. This study provided novel insights into the mechanism of Seed Shattering in E. sibiricus.
Aldo Merotto - One of the best experts on this subject based on the ideXlab platform.
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nucleotide variability and gene expression reveal new putative genes related to Seed Shattering in weedy rice
Annals of Applied Biology, 2015Co-Authors: Anderson Luis Nunes, Carla Andrea Delatorre, Catarine Markus, Aldo MerottoAbstract:Seed Shattering is one of the main traits related with the domestication of cultivated rice and with the invasiveness and persistence of weedy rice. Two independent studies in 2006 have indicated that qSH1 in Japonica and Sh4 in Indica rice are major genes governing this trait. However, a wide variation of Seed Shattering occurs in weedy rice ecotypes from the same geographic region and even within the same ecotype. The aim of this study was to evaluate the nucleotide variability of known and putative genes related to Seed Shattering in cultivated rice and to identify and validate new genes related to this trait in weedy rice. The qSH1 gene was not associated with Seed Shattering in the evaluated genotypes. The nucleotide variability of the genes Os01g0849100 and Os08g0512400, previously identified based on a genome-wide resequencing study, was related to Seed Shattering in rice. The nucleotide variability of three single nucleotide polymorphisms (SNPs) of the OsXTH8 gene, which is related to cell wall biosynthesis, was not associated with Seed Shattering. However, the high expression of this gene was related to the occurrence of this trait. This study evaluated jointly a series of genes involved in rice Seed Shattering and indicated that the genes OsXTH8, Os08g0512400 and Os01g0849100 are important for the regulation of this trait in weedy rice in addition to previously described genes. Seed Shattering in weedy rice has a more complex regulation than in cultivated rice where few major genes were identified.
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gene expression related to Seed Shattering and the cell wall in cultivated and weedy rice
Plant Biology, 2014Co-Authors: Anderson Luis Nunes, Carla Andrea Delatorre, Aldo MerottoAbstract:: Seed Shattering is an evolutionary trait that is essential to the survival of wild and weedy rice. Discovery of the qSH1 gene in rice subspecies Japonica and Sh4 in the rice subspecies Indica indicated the possibility that Seed Shattering is governed by major genes in a qualitative manner. However, observation of the large variability of Seed Shattering in weedy rice has led us to hypothesise that other genes related to abscission layer integrity could also be important in the regulation of Seed Shattering in rice. Gene expression 10 days after pollination and nucleotide composition revealed that qSH1 and Sh4 that are described as major players in Seed Shattering were not important in weedy rice. High expression of the gene OsCPL1 was positively associated with the occurrence of high Seed Shattering in weedy rice, which did not concur in previous studies of cultivated rice. This result is related to the absence of four SNPs and an indel in the OsCPL1 gene in weedy rice that are related to Seed Shattering in previous studies. Analysis of the expression of six genes related to cell wall synthesis/degradation revealed the importance of the genes OsXTH8 and OsCel9D in Seed Shattering in weedy rice. Therefore, in addition to qSH1 and Sh4, the genes OsCPL1, OsXTH8 and OsCel9D should be considered in studies of rice evolution and in the development of mitigation approaches of gene flow in transgenic rice.
Junchao Zhang - One of the best experts on this subject based on the ideXlab platform.
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Construction of the first high-density genetic linkage map and identification of Seed yield-related QTLs and candidate genes in Elymus sibiricus, an important forage grass in Qinghai-Tibet Plateau
BMC Genomics, 2019Co-Authors: Zongyu Zhang, Junchao Zhang, Yongqiang Zhao, Na Wang, Yanrong WangAbstract:Elymus sibiricus is an ecologically and economically important perennial, self-pollinated, and allotetraploid (StStHH) grass, widely used for forage production and animal husbandry in Western and Northern China. However, it has low Seed yield mainly caused by Seed Shattering, which makes Seed production difficult for this species. The goals of this study were to construct the high-density genetic linkage map, and to identify QTLs and candidate genes for Seed-yield related traits. An F2 mapping population of 200 individuals was developed from a cross between single genotype from “Y1005” and “ZhN06”. Specific-locus amplified fragment sequencing (SLAF-seq) was applied to construct the first genetic linkage map. The final genetic map included 1971 markers on the 14 linkage groups (LGs) and was 1866.35 cM in total. The length of each linkage group varied from 87.67 cM (LG7) to 183.45 cM (LG1), with an average distance of 1.66 cM between adjacent markers. The marker sequences of E. sibiricus were compared to two grass genomes and showed 1556 (79%) markers mapped to wheat, 1380 (70%) to barley. Phenotypic data of eight Seed-related traits (2016–2018) were used for QTL identification. A total of 29 QTLs were detected for eight Seed-related traits on 14 linkage groups, of which 16 QTLs could be consistently detected for two or three years. A total of 6 QTLs were associated with Seed Shattering. Based on annotation with wheat and barley genome and transcriptome data of abscission zone in E. sibiricus, we identified 30 candidate genes for Seed Shattering, of which 15, 7, 6 and 2 genes were involved in plant hormone signal transcription, transcription factor, hydrolase activity and lignin biosynthetic pathway, respectively. This study constructed the first high-density genetic linkage map and identified QTLs and candidate genes for Seed-related traits in E. sibiricus. Results of this study will not only serve as genome-wide resources for gene/QTL fine mapping, but also provide a genetic framework for anchoring sequence scaffolds on chromosomes in future genome sequence assembly of E. sibiricus.
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elymus nutans genes for Seed Shattering and candidate gene derived est ssr markers for germplasm evaluation
BMC Plant Biology, 2019Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu ZhangAbstract:Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial Seed production due to serious Seed Shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with Seed Shattering, explore candidate genes involved in Seed Shattering and identify candidate gene-based EST-SSR markers for germplasm evaluation. cDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and Seed Shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting Seed Shattering habit. The dendrogram based on molecular data showed that most accessions with similar Seed Shattering degree tended to group together. The expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future.
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Hybrid identification and genetic variation of Elymus sibiricus hybrid populations using EST-SSR markers.
Hereditas, 2017Co-Authors: Xuhong Zhao, Junchao Zhang, Zongyu Zhang, Yanrong WangAbstract:Elymus sibiricus is an important native grass in Qinghai-Tibetan Plateau. Seed Shattering is a serious problem for E. sibiricus, especially at harvest time. Cross breeding is an effective way to create new varieties with beneficial characteristic or improved traits, and to broaden genetic base. In this study, we created five hybrid populations by crossing seven E. sibiricus genotypes that have Seed Shattering variation. Then, nine EST-SSR primers were used for hybrid identification based on DNA fingerprinting, and genetic diversity analysis of hybrid populations and their respective parents. A total of 15 hybrids were identified. An analysis of amplified polymorphic bands among genuine hybrids and their respective parents revealed mainly two types of markers: 1) hybrids shared bands exclusively amplified in both parents; 2)hybrids shared bands exclusively amplified in male parents. For each hybrid population, the total number of amplified bands ranged from 37 to 57, the percentage of polymorphism varied from 65.12% to 75.68%, with an average of 70.51%. Novel bands found in each hybrid population varied from 0 to 9 bands, suggesting an occurrence of rearrangements in the hybrid population. The structure analysis revealed that all hybrid populations and parents were assigned to eight groups. The principal coordinate analysis (PCoA) showed similar results. In general, this study proved EST-SSR markers are efficient for hybrid identification, and suggested more genetic variation could be captured in hybrid populations by crossing breeding.
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transcriptome profiling of elymus sibiricus an important forage grass in qinghai tibet plateau reveals novel insights into candidate genes that potentially connected to Seed Shattering
BMC Plant Biology, 2017Co-Authors: Junchao Zhang, Xuhong Zhao, Zongyu Zhang, Yanrong WangAbstract:Elymus sibiricus is an important forage grass in semi-arid regions, but it is difficult to grow for commercial Seed production due to high Seed Shattering. To better understand the underlying mechanism and explore the putative genes related to Seed Shattering, we conducted a combination of morphological, histological, physiochemical and transcriptome analysis on two E. sibiricus genotypes (XH09 and ZhN03) that have contrasting Seed Shattering. The results show that Seed Shattering is generally caused by a degradation of the abscission layer. Early degradation of abscission layers was associated with the increased Seed Shattering in high Seed Shattering genotype XH09. Two cell wall degrading enzymes, cellulase (CE) and polygalacturonase (PG), had different activity in the abscission zone, indicating their roles in differentiation of abscission layer. cDNA libraries from abscission zone tissue of XH09 and ZhN03 at 7 days, 21 days and 28 days after heading were constructed and sequenced. A total of 86,634 unigenes were annotated and 7110 differentially expressed transcripts (DETs) were predicted from “XH09-7 vs ZhN03-7”, “XH09-21 vs ZhN03-21” and “XH09-28 vs ZhN03-28”, corresponding to 2058 up-regulated and 5052 down-regulated unigenes. The expression profiles of 10 candidate transcripts involved in cell wall-degrading enzymes, lignin biosynthesis and phytohormone activity were validated using quantitative real-time PCR (qRT-PCR), 8 of which were up-regulated in low Seed Shattering genotype ZhN03, suggesting these genes may be associated with reduction of Seed Shattering. The expression data generated in this study provides an important resource for future molecular biological research in E. sibiricus.
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histological characteristics cell wall hydrolytic enzymes activity and candidate genes expression associated with Seed Shattering of elymus sibiricus accessions
Frontiers in Plant Science, 2017Co-Authors: Xuhong Zhao, Junchao Zhang, Zongyu Zhang, Yanrong WangAbstract:Elymus sibiricus (siberian wildrye) is a perennial, cool-season, self-pollinating, and allotetraploid grass. As an economically important species, it has been widely grown and used for pasture and hay in northern China. Because of serious Seed Shattering, however, E. sibiricus is difficult to grow for commercial Seed production. To better understand the underlying mechanism of Seed Shattering, we investigated the differences in Seed Shattering of cultivars and wild accessions in relation to morphological and genetic diversity, histological characteristics, lignin staining, cell wall hydrolytic enzymes activity and candidate genes expressions. We found high level of morphological and genetic diversity among E. sibiricus accessions. In general, cultivars had higher average pedicel breaking tensile strength (BTS) value than wild accessions, of which PI655199 had the highest average BTS value (144.51 gf) and LQ04 had the lowest average BTS value (47.17 gf) during Seed development. Seed Shattering showed a significant correlation with Seed length (SL), awn length (AL) and 1000-Seed weight (KW). Seed Shattering was caused by degradation of abscission layers that formed at early heading stage, and degradation of abscission layers occurred at 14 days after heading (DAH). Histological analysis of abscission zone showed a smooth fracture surface on the rachilla in high Seed Shattering genotype, suggesting higher degradation degree of abscission layers. This may resulted from the increased cellulase (CE) and polygalacturonase (PG) activity found in abscission zone at Seed physiological maturity. Staining of pedicels of two contrasting genotypes suggested more lignin deposition in low Seed Shattering genotype may play an role in resistance of Seed Shattering. Furthermore, candidate genes that involved in cell wall-degrading enzyme and lignin biosynthesis were differentially expressed in abscission zone, indicating the involvement and role in Seed Shattering. This study provided novel insights into the mechanism of Seed Shattering in E. sibiricus.