scholarly journals Association Mapping and Domestication Analysis to Dissect Genetic Improvement Process of Upland Cotton Yield-Related Traits in China

2021 ◽  
Author(s):  
GUO Chunping ◽  
PAN Zhenyuan ◽  
YOU Chunyuan ◽  
ZHOU Xiaofeng ◽  
HUANG Cong ◽  
...  
Keyword(s):  
Association Mapping ◽  
Cotton Fiber ◽  
Upland Cotton ◽  
Genetic Improvement ◽  
Genetic Basis ◽  
Agronomic Traits ◽  
Complex Trait ◽  
Tissue Expression ◽  
Cotton Yield ◽  
Fiber Yield

Abstract BackgroundCotton fiber yield is a complex trait, which can be influenced by multiple agronomic traits. Unravelling the genetic basis of cotton fiber yield related traits contributes to genetic improvement of cotton fiber. ResultsIn this study, 503 upland cotton varieties covering the 4 breeding stages in China were used to for association mapping and domestication analysis of upland cotton yield-related traits in China. 140 quantitative trait loci (QTLs) significantly associated with ten fiber yield related traits were identified, among which, 29 QTLs showed an increasing trend contribution to cotton yield-related traits from BS1 to BS4, and 26 QTLs showed decreased trend effect. 4 favorable alleles of 9 major QTLs (R2≥3) were strongly selected during the breeding stages, and the candidate genes of the 4 strongly selected alleles were predicated according to the gene function annotation and tissue expression data. ConclusionsThe study not only uncovers the genetic basis of 10 cotton yield related traits, but also provides genetic evidence for cotton improvement during the cotton breeding process in China.

scholarly journals Association mapping and domestication analysis to dissect genetic improvement process of upland cotton yield-related traits in China

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Chunping GUO ◽  
Zhenyuan PAN ◽  
Chunyuan YOU ◽  
Xiaofeng ZHOU ◽  
Cong HUANG ◽  
...  
Keyword(s):  
Association Mapping ◽  
Cotton Fiber ◽  
Upland Cotton ◽  
Genetic Improvement ◽  
Genetic Basis ◽  
Agronomic Traits ◽  
Complex Trait ◽  
Tissue Expression ◽  
Cotton Yield ◽  
Fiber Yield

Abstract Background Cotton fiber yield is a complex trait, which can be influenced by multiple agronomic traits. Unravelling the genetic basis of cotton fiber yield-related traits contributes to genetic improvement of cotton. Results In this study, 503 upland cotton varieties covering the four breeding stages (BS1–BS4, 1911–2011) in China were used for association mapping and domestication analysis. One hundred and forty SSR markers significantly associated with ten fiber yield-related traits were identified, among which, 29 markers showed an increasing trend contribution to cotton yield-related traits from BS1 to BS4, and 26 markers showed decreased trend effect. Four favorable alleles of 9 major loci (R2 ≥ 3) were strongly selected during the breeding stages, and the candidate genes of the four strongly selected alleles were predicated according to the gene function annotation and tissue expression data. Conclusions The study not only uncovers the genetic basis of 10 cotton yield-related traits but also provides genetic evidence for cotton improvement during the cotton breeding process in China.

scholarly journals Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

2020 ◽  
Author(s):  
De Zhu ◽  
Ximei Li ◽  
Zhiwei Wang ◽  
Chunyuan You ◽  
Xinhui Nie ◽  
...  
Keyword(s):  
Upland Cotton ◽  
Genetic Improvement ◽  
Agronomic Traits ◽  
Physical Map ◽  
Leaf Shape ◽  
Interval Length ◽  
Phenotypic Variance ◽  
Nucleotide Polymorphisms ◽  
Substitution Lines ◽  
Multiple Alleles

Abstract Background: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization.Results: In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1,211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions: This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

scholarly journals Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

2020 ◽  
Author(s):  
De Zhu ◽  
Ximei Li ◽  
Zhiwei Wang ◽  
Chunyuan You ◽  
Xinhui Nie ◽  
...  
Keyword(s):  
Upland Cotton ◽  
Genetic Improvement ◽  
Oil Content ◽  
Agronomic Traits ◽  
Physical Map ◽  
Leaf Shape ◽  
Cottonseed Oil ◽  
Interval Length ◽  
Phenotypic Variance ◽  
Multiple Alleles

Abstract Background: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTLs) in interspecific hybridization. Results: In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1,211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions: This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

Association mapping for seed cotton yield, yield components and fibre quality traits in upland cotton (Gossypium hirsutum L.) genotypes

2017 ◽  
Vol 136 (6) ◽  
pp. 958-968 ◽  
Author(s):  
Suresh S. Handi ◽  
Ishwarappa S. Katageri ◽  
Sateesh Adiger ◽  
Mangesh P. Jadhav ◽  
Sivarama P. Lekkala ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Association Mapping ◽  
Yield Components ◽  
Upland Cotton ◽  
Quality Traits ◽  
Fibre Quality ◽  
Cotton Yield ◽  
Seed Cotton ◽  
Gossypium Hirsutum L ◽  
Seed Cotton Yield

scholarly journals Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton

2020 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
Lisheng Bao ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Transcriptome Analysis ◽  
Upland Cotton ◽  
Tissue Expression ◽  
Cotton Yield ◽  
Comparative Transcriptome ◽  
Seed Cotton ◽  
Comparative Transcriptome Analysis ◽  
Seed Cotton Yield ◽  
Efficient Breeding

Abstract Background Utilization of heterosis has greatly improved the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization produces superior yield in upland cotton is critical for efficient breeding programs. Results In this study, high, medium, and low hybrids varying in the level of yield heterosis were screened based on field experimentation of different years and locations. Phenotypically, high hybrid produced a mean of 14% more seed cotton yield than its better parent. Whole-genome RNA sequencing of these hybrids and their four inbred parents was performed using different tissues of the squaring stage. Comparative transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis identified majority of hybrids DEGs were biased towards parent like expressions. An array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation had more functional annotations in hybrids. Sugar metabolic and plant hormone signal transduction pathways were most enriched in each hybrid. Further, these two pathways had most mapped DEGs on known seed cotton yield QTLs. Integration of transcriptome, QTLs, and gene co-expression network analysis discovered genes Gh_A03G1024, Gh_D08G1440, Gh_A08G2210, Gh_A12G2183, Gh_D07G1312, Gh_D08G1467, Gh_A03G0889, Gh_A08G2199, and Gh_D05G0202 displayed a complex regulatory network of many interconnected genes. qRT-PCR of these DEGs was performed to ensure the accuracy of RNA-Seq data. Conclusions Through genome-wide comparative transcriptome analysis, the current study identified nine key genes and pathways associated with biological process of yield heterosis in upland cotton. Our results and data resources provide novel insights and will be useful for dissecting the molecular mechanism of yield heterosis in cotton

scholarly journals Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton

2020 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
Lisheng Bao ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Transcriptome Analysis ◽  
Upland Cotton ◽  
Tissue Expression ◽  
Cotton Yield ◽  
Comparative Transcriptome ◽  
Seed Cotton ◽  
Comparative Transcriptome Analysis ◽  
Seed Cotton Yield ◽  
Efficient Breeding

Abstract Background: Utilization of heterosis has greatly improved the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization produces superior yield in upland cotton is critical for efficient breeding programs. Results: In this study, high, medium, and low hybrids varying in the level of yield heterosis were screened based on field experimentation of different years and locations. Phenotypically, high hybrid produced a mean of 14% more seed cotton yield than its better parent. Whole-genome RNA sequencing of these hybrids and their four inbred parents was performed using different tissues of the squaring stage. Comparative transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis identified majority of hybrids DEGs were biased towards parent like expressions. An array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation had more functional annotations in hybrids. Sugar metabolic and plant hormone signal transduction pathways were most enriched in each hybrid. Further, these two pathways had most mapped DEGs on known seed cotton yield QTLs. Integration of transcriptome, QTLs, and gene co-expression network analysis discovered genes Gh_A03G1024, Gh_D08G1440, Gh_A08G2210, Gh_A12G2183, Gh_D07G1312, Gh_D08G1467, Gh_A03G0889, Gh_A08G2199, and Gh_D05G0202 displayed a complex regulatory network of many interconnected genes. qRT-PCR of these DEGs was performed to ensure the accuracy of RNA-Seq data. Conclusions: Through genome-wide comparative transcriptome analysis, the current study identified nine key genes and pathways associated with biological process of yield heterosis in upland cotton. Our results and data resources provide novel insights and will be useful for dissecting the molecular mechanism of yield heterosis in cotton.

scholarly journals Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton

2020 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
Lisheng Bao ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Transcriptome Analysis ◽  
Upland Cotton ◽  
Tissue Expression ◽  
Cotton Yield ◽  
Comparative Transcriptome ◽  
Seed Cotton ◽  
Comparative Transcriptome Analysis ◽  
Seed Cotton Yield ◽  
Field Experimentation

Abstract Background: Utilization of heterosis has greatly enhanced the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization in cotton produces superior yield is critical for efficient plant breeding. Results: With the whole-genome RNA sequencing, here, high, medium, and low hybrids varying in level of yield heterosis were screened based on different years and locations field experimentation. Phenotypically, high Department showed a mean of 14% more seed cotton yield than its better parent. A total of 63 samples comprised of different squaring stage tissues of three hybrids and four their inbred parents were used to perform transcriptomic analysis. A comparison of transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis exposed the majority of hybrids DEGs followed parent like expressions. Functional annotations identified an array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation. Starch and sucrose metabolism and plant hormone signal transduction pathways were most enriched in each hybrid. Further, these two pathways had most mapped DEGs on known seed cotton yield QTLs. Integration of transcriptome, QTLs, and gene co-expression network analysis raveled genes GhBZR1, GhASK8, At3g43860, GhGBSS1, GhAPL2, GhMPK4, GhPHO1, GhJAZ10, and GhCRR21 displayed a complex regulatory network of many interconnected genes. qRT-PCR of these DEGs was performed to ensure the accuracy of RNA-Seq data. Conclusions: Through genome-wide comparative transcriptome analysis, the current study provides novel insights about phenomics and genomics of heterosis in upland cotton. Our results and data resources will be useful for dissecting the molecular mechanism of yield heterosis in cotton.

Association mapping analysis of fiber yield and quality traits in Upland cotton (Gossypium hirsutum L.)

2017 ◽  
Vol 292 (6) ◽  
pp. 1267-1280 ◽  
Author(s):  
Mulugeta Seyoum Ademe ◽  
Shoupu He ◽  
Zhaoe Pan ◽  
Junling Sun ◽  
Qinglian Wang ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Association Mapping ◽  
Upland Cotton ◽  
Quality Traits ◽  
Gossypium Hirsutum L ◽  
Yield And Quality ◽  
Fiber Yield ◽  
Mapping Analysis

scholarly journals Genome-wide association study of micronaire using a natural population of representative upland cotton (Gossypium hirsutum L.)

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jikun SONG ◽  
Wenfeng PEI ◽  
Jianjiang MA ◽  
Shuxian YANG ◽  
Bing JIA ◽  
...  
Keyword(s):  
Association Study ◽  
Cotton Fiber ◽  
Upland Cotton ◽  
Genetic Improvement ◽  
Genome Wide Association Study ◽  
Expression Patterns ◽  
Snp Array ◽  
Genome Wide Association ◽  
Internal Quality ◽  
Genome Wide

Abstract Background Micronaire is a comprehensive index reflecting the fineness and maturity of cotton fiber. Micronaire is one of the important internal quality indicators of the cotton fiber and is closely related to the value of the cotton fiber. Understanding the genetic basis of micronaire is required for the genetic improvement of the trait. However, the genetic architecture of micronaire at the genomic level is unclear. The present genome-wide association study (GWAS) aimed to identify the genetic mechanism of the micronaire trait in 83 representative upland cotton lines grown in multiple environments. Results GWAS of micronaire used 83 upland cotton accessions assayed by a Cotton 63 K Illumina Infinium single nucleotide polymorphism (SNP) array. A total of 11 quantitative trait loci (QTLs) for micronaire were detected on 10 chromosomes. These 11 QTLs included 27 identified genes with specific expression patterns. A novel QTL, qFM-A12–1, included 12 significant SNPs, and GhFLA9 was identified as a candidate gene based on haplotype block analysis and on strong and direct linkage disequilibrium between the significantly related SNPs and gene. GhFLA9 was expressed at a high level during secondary wall thickening at 20∼25 days post-anthesis. The expression level of GhFLA9 was significantly higher in the low micronaire line (Msco-12) than that in the high micronaire line (Chuangyou-9). Conclusions This study provides a genetic reference for genetic improvement of cotton fiber micronaire and a foundation for verification of the functions of GhFLA9.

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