Dataset Information

GWAS Analysis and QTL Identification of Fiber Quality Traits and Yield Components in Upland Cotton Using Enriched High-Density SNP Markers.

ABSTRACT: It is of great importance to identify quantitative trait loci (QTL) controlling fiber quality traits and yield components for future marker-assisted selection (MAS) and candidate gene function identifications. In this study, two kinds of traits in 231 F_6:8 recombinant inbred lines (RILs), derived from an intraspecific cross between Xinluzao24, a cultivar with elite fiber quality, and Lumianyan28, a cultivar with wide adaptability and high yield potential, were measured in nine environments. This RIL population was genotyped by 122 SSR and 4729 SNP markers, which were also used to construct the genetic map. The map covered 2477.99 cM of hirsutum genome, with an average marker interval of 0.51 cM between adjacent markers. As a result, a total of 134 QTLs for fiber quality traits and 122 QTLs for yield components were detected, with 2.18-24.45 and 1.68-28.27% proportions of the phenotypic variance explained by each QTL, respectively. Among these QTLs, 57 were detected in at least two environments, named stable QTLs. A total of 209 and 139 quantitative trait nucleotides (QTNs) were associated with fiber quality traits and yield components by four multilocus genome-wide association studies methods, respectively. Among these QTNs, 74 were detected by at least two algorithms or in two environments. The candidate genes harbored by 57 stable QTLs were compared with the ones associated with QTN, and 35 common candidate genes were found. Among these common candidate genes, four were possibly "pleiotropic." This study provided important information for MAS and candidate gene functional studies.

SUBMITTER: Liu R

PROVIDER: S-EPMC6157485 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Publications

GWAS Analysis and QTL Identification of Fiber Quality Traits and Yield Components in Upland Cotton Using Enriched High-Density SNP Markers.

Liu Ruixian R Gong Juwu J Xiao Xianghui X Zhang Zhen Z Li Junwen J Liu Aiying A Lu Quanwei Q Shang Haihong H Shi Yuzhen Y Ge Qun Q Iqbal Muhammad S MS Deng Xiaoying X Li Shaoqi S Pan Jingtao J Duan Li L Zhang Qi Q Jiang Xiao X Zou Xianyan X Hafeez Abdul A Chen Quanjia Q Geng Hongwei H Gong Wankui W Yuan Youlu Y

Frontiers in plant science 20180913

It is of great importance to identify quantitative trait loci (QTL) controlling fiber quality traits and yield components for future marker-assisted selection (MAS) and candidate gene function identifications. In this study, two kinds of traits in 231 F<sub>6:8</sub> recombinant inbred lines (RILs), derived from an intraspecific cross between Xinluzao24, a cultivar with elite fiber quality, and Lumianyan28, a cultivar with wide adaptability and high yield potential, were measured in nine environ ...[more]

PMID: 30283462

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Project description:BackgroundCotton (Gossypium spp.) fiber yield is one of the key target traits, and improved fiber yield has always been thought of as an important objective in the breeding programs and production. Although some studies had been reported for the understanding of genetic bases for cotton yield-related traits, the detected quantitative trait loci (QTL) for the traits is still very limited. To uncover the whole-genome QTL controlling three yield-related traits in upland cotton (Gossypium hirsutum L.), phenotypic traits were investigated under four planting environments and 9244 single-nucleotide polymorphism linkage disequilibrium block (SNPLDB) markers were developed in an association panel consisting of 315 accessions.ResultsA total of 53, 70 and 68 significant SNPLDB loci associated with boll number (BN), boll weight (BW) and lint percentage (LP), were respectively detected through a restricted two-stage multi-locus multi-allele genome-wide association study (RTM-GWAS) procedure in multiple environments. The haplotype/allele effects of the significant SNPLDB loci were estimated and the QTL-allele matrices were organized for offering the abbreviated genetic composition of the population. Among the significant SNPLDB loci, six of them were simultaneously identified in two or more single planting environments and were thought of as the stable SNPLDB loci. Additionally, a total of 115 genes were annotated in the nearby regions of the six stable SNPLDB loci, and 16 common potential candidate genes controlling target traits of them were predicted by two RNA-seq data. One of 16 genes (GH_D06G2161) was mainly expressed in the early ovule-development stages, and the stable SNPLDB locus (LDB_19_62926589) was mapped in its promoter region.ConclusionThis study identified the QTL alleles and candidate genes that could provide important insights into the genetic basis of yield-related traits in upland cotton and might facilitate breeding cotton varieties with high yield.

Project description:BackgroundQuantitative trait loci (QTL) mapping provides a powerful tool to unravel the genetic bases of cotton yield and its components, as well as their heterosis. In the present study, the genetic basis underlying inbreeding depression and heterosis for yield and yield components of upland cotton was investigated in recombinant inbred line (RIL), immortalized F2 (IF2), and two backcross (BCF1) populations based on a high-density SNP linkage map across four environments.ResultsSignificant inbreeding depression of fruit branches per plant (FB), boll numbers per plant (BN), seed cotton yield (SY), and lint yield (LY) in RIL population and high levels of heterosis for SY, LY, and boll weight (BW) in IF2 and two BCF1 populations were observed. A total of 285 QTLs were identified in the four related populations using a composite interval mapping approach. In the IF2 population, 26.60% partially dominant (PD) QTLs and 71.28% over-dominant (OD) QTLs were identified. In two BCF1 populations, 42.41% additive QTLs, 4.19% PD QTLs, and 53.40% OD QTLs were detected. For multi-environment analysis, phenotypic variances (PV) explained by e-QTLs were higher than those by m-QTLs in each of the populations, and the average PV of m-QTLs and e-QTLs explained by QTL?×?environment interactions occupied a considerable proportion of total PV in all seven datasets.ConclusionsAt the single-locus level, the genetic bases of heterosis varied in different populations. Partial dominance and over-dominance were the main cause of heterosis in the IF2 population, while additive effects and over-dominance were the main genetic bases of heterosis in two BCF1 populations. In addition, the various genetic components to heterosis presented trait specificity. In the multi-environment model analysis, epistasis was a common feature of most loci associated with inbreeding depression and heterosis. Furthermore, the environment was a critical factor in the expression of these m-QTLs and e-QTLs. Altogether, additive effects, over-dominance, epistasis and environmental interactions all contributed to the heterosis of yield and its components in upland cotton, with over-dominance and epistasis more important than the others.

Project description:BACKGROUND:Improving fiber quality and yield are the primary research objectives in cotton breeding for enhancing the economic viability and sustainability of Upland cotton production. Identifying the quantitative trait loci (QTL) for fiber quality and yield traits using the high-density SNP-based genetic maps allows for bridging genomics with cotton breeding through marker assisted and genomic selection. In this study, a recombinant inbred line (RIL) population, derived from cross between two parental accessions, which represent broad allele diversity in Upland cotton, was used to construct high-density SNP-based linkage maps and to map the QTLs controlling important cotton traits. RESULTS:Molecular genetic mapping using RIL population produced a genetic map of 3129 SNPs, mapped at a density of 1.41?cM. Genetic maps of the individual chromosomes showed good collinearity with the sequence based physical map. A total of 106 QTLs were identified which included 59 QTLs for six fiber quality traits, 38 QTLs for four yield traits and 9 QTLs for two morphological traits. Sub-genome wide, 57 QTLs were mapped in A sub-genome and 49 were mapped in D sub-genome. More than 75% of the QTLs with favorable alleles were contributed by the parental accession NC05AZ06. Forty-six mapped QTLs each explained more than 10% of the phenotypic variation. Further, we identified 21 QTL clusters where 12 QTL clusters were mapped in the A sub-genome and 9 were mapped in the D sub-genome. Candidate gene analyses of the 11 stable QTL harboring genomic regions identified 19 putative genes which had functional role in cotton fiber development. CONCLUSION:We constructed a high-density genetic map of SNPs in Upland cotton. Collinearity between genetic and physical maps indicated no major structural changes in the genetic mapping populations. Most traits showed high broad-sense heritability. One hundred and six QTLs were identified for the fiber quality, yield and morphological traits. Majority of the QTLs with favorable alleles were contributed by improved parental accession. More than 70% of the mapped QTLs shared the similar map position with previously reported QTLs which suggest the genetic relatedness of Upland cotton germplasm. Identification of QTL clusters could explain the correlation among some fiber quality traits in cotton. Stable and major QTLs and QTL clusters of traits identified in the current study could be the targets for map-based cloning and marker assisted selection (MAS) in cotton breeding. The genomic region on D12 containing the major stable QTLs for micronaire, fiber strength and lint percentage could be potential targets for MAS and gene cloning of fiber quality traits in cotton.

Dataset Information

GWAS Analysis and QTL Identification of Fiber Quality Traits and Yield Components in Upland Cotton Using Enriched High-Density SNP Markers.

Publications

GWAS Analysis and QTL Identification of Fiber Quality Traits and Yield Components in Upland Cotton Using Enriched High-Density SNP Markers.

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