Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome‐wide association study using high‐density SNPs

Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton‐producing and cotton‐consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nationwide population containing 503 G. hirsutum accessions was collected for a genome‐wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high‐density map based on this array were used for genotyping. The 503 G. hirsutum accessions were divided into three subpopulations based on 11 975 quantified polymorphic single‐nucleotide polymorphisms (SNPs). By comparing the genetic structure and phenotypic variation among three genetic subpopulations, seven geographic distributions and four breeding periods, we found that geographic distribution and breeding period were not the determinants of genetic structure. In addition, no obvious phenotypic differentiations were found among the three subpopulations, even though they had different genetic backgrounds. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multieffects in QTLs and interassociations among traits. Thirty‐eight associated regions had pleiotropic effects controlling more than one trait. One candidate gene, Gh_D08G2376, was speculated to control the lint percentage (LP). This GWAS is the first report using high‐resolution SNPs in upland cotton in China to comprehensively investigate agronomic traits, and it provides a fundamental resource for cotton genetic research and breeding.     

A genome-wide association study uncovers novel genomic regions and candidate genes of yield-related traits in upland cotton

Key message

A total of 62 SNPs associated with yield-related traits were identified by a GWAS. Based on significant SNPs, two candidate genes pleiotropically increase lint yield.

Abstract

Improved fibre yield is considered a constant goal of upland cotton (Gossypium hirsutum) breeding worldwide, but the understanding of the genetic basis controlling yield-related traits remains limited. To better decipher the molecular mechanism underlying these traits, we conducted a genome-wide association study to determine candidate loci associated with six yield-related traits in a population of 719 upland cotton germplasm accessions; to accomplish this, we used 10,511 single-nucleotide polymorphisms (SNPs) genotyped by an Illumina CottonSNP63K array. Six traits, including the boll number, boll weight, lint percentage, fruit branch number, seed index and lint index, were assessed in multiple environments; large variation in all phenotypes was detected across accessions. We identified 62 SNP loci that were significantly associated with different traits on chromosomes A07, D03, D05, D09, D10 and D12. A total of 689 candidate genes were screened, and 27 of them contained at least one significant SNP. Furthermore, two genes (Gh_D03G1064 and Gh_D12G2354) that pleiotropically increase lint yield were identified. These identified SNPs and candidate genes provide important insights into the genetic control underlying high yields in G. hirsutum, ultimately facilitating breeding programmes of high-yielding cotton.

     

Population genomics reveals a fine‐scale recombination landscape for genetic improvement of cotton

Recombination breaks up ancestral linkage disequilibrium, creates combinations of alleles, affects the efficiency of natural selection, and plays a major role in crop domestication and improvement. However, there is little knowledge regarding the variation in the population‐scaled recombination rate in cotton. We constructed recombination maps and characterized the difference in the genomic landscape of the population‐scaled recombination rate between Gossypium hirsutum and G. arboreum and sub‐genomes based on the 381 sequenced G. hirsutum and 215 G. arboreum accessions. Comparative genomics identified large structural variations and syntenic genes in the recombination regions, suggesting that recombination was related to structural variation and occurred preferentially in the distal chromosomal regions. Correlation analysis indicated that recombination was only slightly affected by geographical distribution and breeding period. A genome‐wide association study (GWAS) was performed with 15 agronomic traits using 267 cotton accessions and identified 163 quantitative trait loci (QTL) and an important candidate gene (Ghir_COL2) for early maturity traits. Comparative analysis of recombination and a GWAS revealed that the QTL of fibre quality traits tended to be more common in high‐recombination regions than were those of yield and early maturity traits. These results provide insights into the population‐scaled recombination landscape, suggesting that recombination contributed to the domestication and improvement of cotton, which provides a useful reference for studying recombination in other species.     

A genome‐wide association study of early‐maturation traits in upland cotton based on the CottonSNP80K array

Genome‐wide association studies (GWASs) efficiently identify genetic loci controlling traits at a relatively high resolution. In this study, variations in major early‐maturation traits, including seedling period (SP), bud period (BP), flower and boll period (FBP), and growth period (GP), of 169 upland cotton accessions were investigated, and a GWAS of early maturation was performed based on a CottonSNP80K array. A total of 49,650 high‐quality single‐nucleotide polymorphisms (SNPs) were screened, and 29 significant SNPs located on chromosomes A6, A7, A8, D1, D2, and D9, were repeatedly identified as associated with early‐maturation traits, in at least two environments or two algorithms. Of these 29 significant SNPs, 1, 12, 11, and 5 were related to SP, BP, FBP, and GP, respectively. Six peak SNPs, TM47967, TM13732, TM20937, TM28428, TM50283, and TM72552, exhibited phenotypic contributions of approximately 10%, which could allow them to be used for marker‐assisted selection. One of these, TM72552, as well as four other SNPs, TM72554, TM72555, TM72558, and TM72559, corresponded to the quantitative trait loci previously reported. In total, 274 candidate genes were identified from the genome sequences of upland cotton and were categorized based on their functional annotations. Finally, our studies identified Gh_D01G0340 and Gh_D01G0341 as potential candidate genes for improving cotton early maturity.     

Identification of candidate genes for key fibre‐related QTLs and derivation of favourable alleles in Gossypium hirsutum recombinant inbred lines with G. barbadense introgressions

Fine mapping QTLs and identifying candidate genes for cotton fibre‐quality and yield traits would be beneficial to cotton breeding. Here, we constructed a high‐density genetic map by specific‐locus amplified fragment sequencing (SLAF‐seq) to identify QTLs associated with fibre‐quality and yield traits using 239 recombinant inbred lines (RILs), which was developed from LMY22 (a high‐yield Gossypium hirsutumL. cultivar) × LY343 (a superior fibre‐quality germplasm with G. barbadenseL. introgressions). The genetic map spanned 3426.57 cM, including 3556 SLAF‐based SNPs and 199 SSR marker loci. A total of 104 QTLs, including 67 QTLs for fibre quality and 37 QTLs for yield traits, were identified with phenotypic data collected from 7 environments. Among these, 66 QTLs were co‐located in 19 QTL clusters on 12 chromosomes, and 24 QTLs were detected in three or more environments and determined to be stable. We also investigated the genomic components of LY343 and their contributions to fibre‐related traits by deep sequencing the whole genome of LY343, and we found that genomic components from G. hirsutum races (which entered LY343 via its G. barbadense parent) contributed more favourable alleles than those from G. barbadense. We further identified six putative candidate genes for stable QTLs, including Gh_A03G1147 (GhPEL6), Gh_D07G1598 (GhCSLC6) and Gh_D13G1921 (GhTBL5) for fibre‐length QTLs and Gh_D03G0919 (GhCOBL4), Gh_D09G1659 (GhMYB4) and Gh_D09G1690 (GhMYB85) for lint‐percentage QTLs. Our results provide comprehensive insight into the genetic basis of the formation of fibre‐related traits and would be helpful for cloning fibre‐development‐related genes as well as for marker‐assisted genetic improvement in cotton.     

Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (Gossypium hirsutum L.)

Although upland cotton (Gossypium hirsutism L.) originated in the tropics, this early maturity cotton can be planted as far north as 46°N in China due to the accumulation of numerous phenotypic and physiological adaptations during domestication. However, how the genome of early maturity cotton has been altered by strong human selection remains largely unknown. Herein, we report a cotton genome variation map generated by the resequencing of 436 cotton accessions. Whole‐genome scans for sweep regions identified 357 putative selection sweeps covering 4.94% (112 Mb) of the upland cotton genome, including 5184 genes. These genes were functionally related to flowering time control, hormone catabolism, ageing and defence response adaptations to environmental changes. A genome‐wide association study (GWAS) for seven early maturity traits identified 307 significant loci, 22.48% (69) of which overlapped with putative selection sweeps that occurred during the artificial selection of early maturity cotton. Several previously undescribed candidate genes associated with early maturity were identified by GWAS. This study provides insights into the genetic basis of early maturity in upland cotton as well as breeding resources for cotton improvement.     

Genome‐wide detection of genetic loci and candidate genes for teat number and body conformation traits at birth in Chinese Sushan pigs

Body conformation at birth and teat number are economically important traits in the pig industry, as these traits are usually explored to evaluate the growth and reproductive potential of piglets. To detect genetic loci and candidate genes for these traits, we performed a GWAS on 269 pigs from a recently developed Chinese breed (Sushan) using 38  128 informative SNPs on the Affymetrix Porcine SNP 55K Array. In total, we detected one genome‐wide significant (P = 1.31e‐6) SNP for teat number on chromosome X and 15 chromosome‐wide significant SNPs for teat number, body weight, body length, chest circumference and cannon circumference at birth on chromosomes 1, 3, 4, 6, 7, 9, 10, 13, 14, 15, 17 and 18. The most significant SNP had an additive effect of 0.74 × total teat number, explaining 20% of phenotypic variance. Five significant SNPs resided in the previously reported quantitative trait loci for these traits and seven significant SNPs had a pleiotropic effect on multiple traits. Intriguingly, 12 of the genes nearest to the significant SNPs are functionally related to body conformation and teat number traits, including SPRED2, MKX, TMSB4X and ESR1. GO analysis revealed that candidate genes proximal to the significant SNPs were enriched in the G‐protein coupled receptor and steroid hormone‐mediated signaling pathway. Our findings shed light on the genetic basis of the measured traits and provide molecular markers especially for the genetic improvement of teat number in Sushan and related pigs.     

A genome-wide association study of early-maturation traits in upland cotton based on the CottonSNP8oK array

Genome-wide association studies(GWASs)efficiently identify genetic loci controlling traits at a relatively high resolution.In this study,variations in major early-maturation traits,including seedling period(SP),bud period(BP),flower and boll period(FBP),and growth period(GP),of 169 upland cotton accessions were investigated,and a GWAS of early maturation was performed based on a CottonSNP80K array.A total of49,650 high-quality single-nucleotide polymorphisms(SNPs)were screened,and 29 significant SNPs located on chromosomes A6,A7,A8,D1,D2,and D9,were repeatedly identified as associated with early-maturation traits,in at least two environments or two algorithms.Of these 29 significant SNPs,1,12,11,and 5 were related to SP,BP,FBP,and GP,respectively.Six peak SNPs,TM47967,TM13732,TM20937,TM28428,TM50283,and TM72552,exhibited phenotypic contributions of approximately 10%,which could allow them to be used for marker-assisted selection.One of these,TM72552,as well as four other SNPs,TM72554,TM72555,TM72558,and TM72559,corresponded to the quantitative trait loci previously reported.In total,274 candidate genes were identified from the genome sequences of upland cotton and were categorized based on their functional annotations.Finally,our studies identified Gh_D01G0340 and Gh_D01G0341 as potential candidate genes for improving cotton early maturity.     

Dissection of the genetic architecture of three seed‐quality traits and consequences for breeding in Brassica napus

Genome‐wide association studies (GWASs) combining high‐throughput genome resequencing and phenotyping can accelerate the dissection of genetic architecture and identification of genes for plant complex traits. In this study, we developed a rapeseed genomic variation map consisting of 4 542 011 SNPs and 628 666 INDELs. GWAS was performed for three seed‐quality traits, including erucic acid content (EAC), glucosinolate content (GSC) and seed oil content (SOC) using 3.82 million polymorphisms in an association panel. Six, 49 and 17 loci were detected to be associated with EAC, GSC and SOC in multiple environments, respectively. The mean total contribution of these loci in each environment was 94.1% for EAC and 87.9% for GSC, notably higher than that for SOC (40.1%). A high correlation was observed between phenotypic variance and number of favourable alleles for associated loci, which will contribute to breeding improvement by pyramiding these loci. Furthermore, candidate genes were detected underlying associated loci, based on functional polymorphisms in gene regions where sequence variation was found to correlate with phenotypic variation. Our approach was validated by detection of well‐characterized FAE1 genes at each of two major loci for EAC on chromosomes A8 and C3, along with MYB28 genes at each of three major loci for GSC on chromosomes A9, C2 and C9. Four novel candidate genes were detected by correlation between GSC and SOC and observed sequence variation, respectively. This study provides insights into the genetic architecture of three seed‐quality traits, which would be useful for genetic improvement of B. napus.     

Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton

Key message

Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton.

Abstract

A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block. Furthermore, 21 candidate genes for plant architecture were predicted in a 0.95-Mb region including the four peak SNPs. One of these genes (Gh_D03G0922) was near the significant SNP D03_31584163 (8.40 kb), and its Arabidopsis homologs contain MADS-box domains that might be involved in plant growth and development. qRT-PCR showed that the expression of Gh_D03G0922 was upregulated in the apical buds and young leaves of the short and compact cotton varieties, and virus-induced gene silencing (VIGS) proved that the silenced plants exhibited increased PH. These results indicate that Gh_D03G0922 is likely the candidate gene for PH in cotton. The genetic variations and candidate genes identified in this study lay a foundation for cultivating moderately short and compact varieties in future Chinese cotton-breeding programs.

     

Genome‐wide association study for semen traits of the bulls in Chinese Holstein

A genome‐wide association study (GWAS) was performed to identify markers and candidate genes for five semen traits in the Holstein bull population in China. The analyzed dataset consisted of records from 692 bulls from eight bull stations; each bull was genotyped using the Illumina BovineSNP50 BeadChip. Association tests between each trait and the 41 188 informative high‐quality SNPs were achieved with gapit software. In total, 19 suggestive significant SNPs, partly located within the reported QTL regions or within or close to the reported candidate genes, associated with five semen traits were detected. By combining our GWAS results with the biological functions of these genes, eight novel promising candidate genes, including ETNK1, PDE3A, PDGFRB, CSF1R, WT1, DSCAML1, SOD1 and RUNX2, were identified that potentially relate to semen traits. Our findings may provide a basis for further research on the genetic mechanism of semen traits and marker‐assisted selection of such traits in Holstein bulls.     

Genome‐wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China

Bread wheat is a leading cereal crop worldwide. Limited amount of superior allele loci restricted the progress of molecular improvement in wheat breeding. Here, we revealed new allelic variation distribution for 13 yield‐related traits in series of genome‐wide association studies (GWAS) using the wheat 90K genotyping assay, characterized in 163 bread wheat cultivars. Agronomic traits were investigated in 14 environments at three locations over 3 years. After filtering SNP data sets, GWAS using 20 689 high‐quality SNPs associated 1769 significant loci that explained, on average, ~20% of the phenotypic variation, both detected already reported loci and new promising genomic regions. Of these, repetitive and pleiotropic SNPs on chromosomes 6AS, 6AL, 6BS, 5BL and 7AS were significantly linked to thousand kernel weight, for example BS00021705_51 on 6BS and wsnp_Ex_c32624_41252144 on 6AS, with phenotypic variation explained (PVE) of ~24%, consistently identified in 12 and 13 of the 14 environments, respectively. Kernel length‐related SNPs were mainly identified on chromosomes 7BS, 6AS, 5AL and 5BL. Plant height‐related SNPs on chromosomes 4DS, 6DL, 2DS and 1BL were, respectively, identified in more than 11 environments, with averaged PVE of ~55%. Four SNPs were confirmed to be important genetic loci in two RIL populations. Based on repetivity and PVE, a total of 41 SNP loci possibly played the key role in modulating yield‐related traits of the cultivars surveyed. Distribution of superior alleles at the 41 SNP loci indicated that superior alleles were getting popular with time and modern cultivars had integrated many superior alleles, especially for peduncle length‐ and plant height‐related superior alleles. However, there were still 19 SNP loci showing less than percentages of 50% in modern cultivars, suggesting they should be paid more attention to improve yield‐related traits of cultivars in the Yellow and Huai wheat region. This study could provide useful information for dissection of yield‐related traits and valuable genetic loci for marker‐assisted selection in Chinese wheat breeding programme.     

Genetic mapping and quantitative trait locus analysis of fiber quality traits using a three-parent composite population in upland cotton (Gossypium hirsutum L.)

Composite cross populations (CP) developed from three or more cultivars/lines are frequently used to improve agronomic and economic traits in crop cultivar development programs. Employing CP in linkage map construction and quantitative trait locus (QTL) mapping may increase the marker density of upland cotton (Gossypium hirsutum L.) genetic maps, exploit more adequate gene resources and facilitate marker-assisted selection (MAS). To construct a relatively high-density map and identify QTL associated with fiber quality traits in upland cotton, three elite upland cultivars/lines, Yumian 1, CRI 35 and 7,235, were used to obtain the segregating population, Yumian 1/CRI 35//Yumian 1/7,235. A genetic map containing 978 simple sequence repeat (SSR) loci and 69 linkage groups was constructed; the map spanned 4,184.4 cM, covering approximately 94.1% of the entire tetraploid cotton genome. A total of 63 QTL were detected, explaining 8.1–55.8% of the total phenotypic variance: 11 QTL for fiber elongation, 16 QTL for fiber length, 9 QTL for fiber micronaire reading, 10 QTL for fiber strength and 17 QTL for fiber length uniformity. The genetic map and QTL detected for fiber quality traits are promising for further breeding programs of upland cotton with improved fiber quality.     

Genomic variation at the tips of the adaptive radiation of Darwin's finches

Adaptive radiation unfolds as selection acts on the genetic variation underlying functional traits. The nature of this variation can be revealed by studying the tips of an ongoing adaptive radiation. We studied genomic variation at the tips of the Darwin's finch radiation; specifically focusing on polymorphism within, and variation among, three sympatric species of the genus Geospiza. Using restriction site‐associated DNA (RAD‐seq), we characterized 32 569 single‐nucleotide polymorphisms (SNPs), from which 11 outlier SNPs for beak and body size were uncovered by a genomewide association study (GWAS). Principal component analysis revealed that these 11 SNPs formed four statistically linked groups. Stepwise regression then revealed that the first PC score, which included 6 of the 11 top SNPs, explained over 80% of the variation in beak size, suggesting that selection on these traits influences multiple correlated loci. The two SNPs most strongly associated with beak size were near genes associated with beak morphology across deeper branches of the radiation: delta‐like 1 homologue (DLK1) and high‐mobility group AT‐hook 2 (HMGA2). Our results suggest that (i) key adaptive traits are associated with a small fraction of the genome (11 of 32 569 SNPs), (ii) SNPs linked to the candidate genes are dispersed throughout the genome (on several chromosomes), and (iii) micro‐ and macro‐evolutionary variation (roots and tips of the radiation) involve some shared and some unique genomic regions.     

Genome-wide association study of milk production traits in a crossbred dairy sheep population using three statistical models

Milk production is one of the most important characteristics of dairy sheep, and the identification of genes affecting milk production traits is critical to understanding the genetics and improve milk production in future generations. Three statistical techniques, namely GWAS, ridge-regression BLUP and BayesC , were used to identify SNPs in significant association with three milk production traits (milk yield, fat yield and protein yield) in a crossbred dairy sheep population. The results suggested that chromosomes 1, 3, 4, 5, 7 and 11 were likely to harbor genes important to milk production because these chromosomes had the greatest top-100-SNP variance contributions on the three milk production traits. The GWAS analysis identified between 74 and 288 genome-wide significant SNP (P < 0.05) whereas the BayesCπ model revealed between six and 63 SNPs, each with >95% posterior probability of inclusion as having a non-zero association effect on at least one of the three milk production traits. Positional candidate genes for milk production in sheep were searched, based on the sheep genomic assembly OAR version 3.1, such as those which map position coincided with or was located within 0.1 Mbp of a genome-wide suggestive or significant SNP. These identified SNPs and candidate genes supported some previous findings and also added new information about genetic markers for genetic improvement of lactation in dairy sheep, but keeping in mind that the majority of these positional candidate genes are not necessarily true causative loci for these traits and future validations are thus necessary.     

Genome‐wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield‐related traits in a Gossypium hirsutum recombinant inbred line population

Cotton is widely cultivated globally because it provides natural fibre for the textile industry and human use. To identify quantitative trait loci (QTLs)/genes associated with fibre quality and yield, a recombinant inbred line (RIL) population was developed in upland cotton. A consensus map covering the whole genome was constructed with three types of markers (8295 markers, 5197.17 centimorgans (cM)). Six fibre yield and quality traits were evaluated in 17 environments, and 983 QTLs were identified, 198 of which were stable and mainly distributed on chromosomes 4, 6, 7, 13, 21 and 25. Thirty‐seven QTL clusters were identified, in which 92.8% of paired traits with significant medium or high positive correlations had the same QTL additive effect directions, and all of the paired traits with significant medium or high negative correlations had opposite additive effect directions. In total, 1297 genes were discovered in the QTL clusters, 414 of which were expressed in two RNA‐Seq data sets. Many genes were discovered, 23 of which were promising candidates. Six important QTL clusters that included both fibre quality and yield traits were identified with opposite additive effect directions, and those on chromosome 13 (qClu‐chr13‐2) could increase fibre quality but reduce yield; this result was validated in a natural population using three markers. These data could provide information about the genetic basis of cotton fibre quality and yield and help cotton breeders to improve fibre quality and yield simultaneously.     

利用海岛棉渐渗系改良陆地棉纤维品质

棉花是世界上种植最广泛的纤维作物,随着人们生活水平的提高和棉纺织工业的发展,对棉花的纤维品质提出了更高的要求。本研究利用渐渗系ZP171为亲本,该材料以陆地棉中棉所8号为遗传背景携带了纤维品质优异的海岛棉Pima90-53片段,构建遗传群体并选育优异种质材料。基于群体在多环境下的纤维品质鉴定结果,发现纤维长度和比强度与其他纤维品质性状间存在显著的相关性,遗传力较高,可稳定遗传;基于方差分析及主成分分析发现,群体内含有丰富的遗传变异且群体可通过4个主成分进行评价;综合上述分析结果,筛选出在纤维长度或者纤维比强度上显著优于中棉所8号的19个株系,为棉花优质育种及纤维品质性状精细定位提供了新材料。     

Genetic mapping and QTL analysis of fiber-related traits in cotton (<Emphasis Type="Italic">Gossypium</Emphasis>)

Cotton, the leading natural fiber crop, is largely produced by two primary cultivated allotetraploid species known as Upland or American cotton (Gossypium hirsutum L.) and Pima or Egyptian cotton (G. barbadense L.). The allotetraploid species diverged from each other and from their diploid progenitors (A or D genome) through selection and domestication after polyploidization. To analyze cotton AD genomes and dissect agronomic traits, we have developed a genetic map in an F₂ population derived from interspecific hybrids between G. hirsutum L. cv. Acala-44 and G. barbadense L. cv. Pima S-7. A total of 392 genetic loci, including 333 amplified fragment length polymorphisms (AFLPs), 47 simple sequence repeats (SSRs), and 12 restriction fragment length polymorphisms (RFLPs), were mapped in 42 linkage groups, which span 3,287 cM and cover approximately 70% of the genome. Using chromosomal aneuploid interspecific hybrids and a set of 29 RFLP and SSR framework markers, we assigned 19 linkage groups involving 223 loci to 12 chromosomes. Comparing four pairs of homoeologous chromosomes, we found that with one exception linkage distances in the A-subgenome chromosomes were larger than those in their D-subgenome homoeologues, reflecting higher recombination frequencies and/or larger chromosomes in the A subgenome. Segregation distortion was observed in 30 out of 392 loci mapped in cotton. Moreover, approximately 29% of the RFLPs behaved as dominant loci, which may result from rapid genomic changes. The cotton genetic map was used for quantitative trait loci (QTL) analysis using composite interval mapping and permutation tests. We detected seven QTLs for six fiber-related traits; five of these were distributed among A-subgenome chromosomes, the genome donor of fiber traits. The detection of QTLs in both the A subgenome in this study and the D subgenome in a previous study suggests that fiber-related traits are controlled by the genes in homoeologous genomes, which are subjected to selection and domestication. Some chromosomes contain clusters of QTLs and presumably contribute to the large amount of phenotypic variation that is present for fiber-related traits.Communicated by J. Dvorak     

Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum)

Brown fibre cotton is an environmental‐friendly resource that plays a key role in the textile industry. However, the fibre quality and yield of natural brown cotton are poor, and fundamental research on brown cotton is relatively scarce. To understand the genetic basis of brown fibre cotton, we constructed linkage and association populations to systematically examine brown fibre accessions. We fine‐mapped the brown fibre region, Lc₁, and dissected it into 2 loci, qBF‐A07‐1 and qBF‐A07‐2. The qBF‐A07‐1 locus mediates the initiation of brown fibre production, whereas the shade of the brown fibre is affected by the interaction between qBF‐A07‐1 and qBF‐A07‐2. Gh_A07G2341 and Gh_A07G0100 were identified as candidate genes for qBF‐A07‐1 and qBF‐A07‐2, respectively. Haploid analysis of the signals significantly associated with these two loci showed that most tetraploid modern brown cotton accessions exhibit the introgression signature of Gossypium barbadense. We identified 10 quantitative trait loci (QTLs) for fibre yield and 19 QTLs for fibre quality through a genome‐wide association study (GWAS) and found that qBF‐A07‐2 negatively affects fibre yield and quality through an epistatic interaction with qBF‐A07‐1. This study sheds light on the genetics of fibre colour and lint‐related traits in brown fibre cotton, which will guide the elite cultivars breeding of brown fibre cotton.     

Association of AFLP and SSR markers with agronomic and fibre quality traits in <Emphasis Type="Italic">Gossypium hirsutum</Emphasis> L.

Molecular markers linked to QTL contributing to agronomic and fibre quality traits would be useful for cotton improvement. We have attempted to tag yield and fibre quality traits with AFLP and SSR markers using F₂ and F₃ populations of a cross between two Gossypium hirsutum varieties, PS56-4 and RS2013. Out of 50 AFLP primer combinations and 177 SSR primer pairs tested, 32 AFLP and four SSR primers were chosen for genotyping F₂ individuals. Marker-trait associations were studied for eight agronomic and five fibre quality traits through simple and multiple regression analysis (MRA) using a set of 92 AFLP polymorphic loci and four SSR markers. Simple linear regression analysis (SLRA) identified 23 markers for eight different traits whereas multiple regression analysis identified 30 markers for at least one of the 13 traits. SSR marker BNL 3502 was consistently identified to be associated with fibre strength. While all the markers identified in SLRA were also detected in MRA, as many as 16 of the 30 markers were identified to be associated with respective traits in both F₂ and F₃ generations. The markers explained up to 41 per cent of phenotypic variation for individual traits. A number of markers were found to be associated with multiple traits suggesting clustering of QTLs for fibre quality traits in cotton.