Genetic dissection of chromosome substitution lines of cotton to discover novel Gossypium barbadense L. alleles for improvement of agronomic traits

We recently released a set of 17 chromosome substitution (CS-B) lines (2n = 52) that contain Gossypium barbadense L. doubled-haploid line ‘3-79’ germplasm systematically introgressed into the Upland inbred ‘TM-1’ of G. hirsutum (L.). TM-1 yields much more than 3-79, but cotton from the latter has superior fiber properties. To explore the use of these quasi-isogenic lines in studying gene interactions, we created a partial diallel among six CS-B lines and the inbred TM-1, and characterized their descendents for lint percentage, boll weight, seedcotton yield and lint yield across four environments. Phenotypic data on the traits were analyzed according to the ADAA genetic model to detect significant additive, dominance, and additive-by-additive epistasis effects at the chromosome and chromosome-by-chromosome levels of CS-B lines. For example, line 3-79 had the lowest boll weight, seedcotton yield and lint yield, but CS-B22Lo homozygous dominance genetic effects on seedcotton and lint yield were nearly four times those of TM-1, and its hybrids with TM-1 had the highest additive-by-additive epistatic effects on seedcotton and lint yield. CS-B14sh, 17, 22Lo and 25 produced positive homozygous dominance effects on lint yield, whereas doubly heterozygous combinations of CS-B14sh with CS-B17, 22Lo and 25 produced negative dominance effects, suggesting that epistatic effects between genes in these chromosomes strongly affect lint yield. The results underscore the opportunities to systematically identify genomic regions harboring genes that impart agronomically significant effects via epistatic interactions. The chromosome-by-chromosome approach significantly complements other strategies to detect and quantify epistatic interaction effects, and the quasi-isogenic nature of families and lines from CS-B intermatings will facilitate high-resolution localization, development of markers for selection and map-assisted identification of genes involved in strong epistatic effects.     

Delineation of interspecific epistasis on fiber quality traits in Gossypium hirsutum by ADAA analysis of intermated G. barbadense chromosome substitution lines

Genetic diversity is the foundation of any crop improvement program, but the most cultivated Upland cotton [Gossypium hirsutum L., 2n?=?52, genomic formula?2(AD)₁] has a very narrow gene pool resulting from its evolutionary origin and domestication history. Cultivars of this cotton species (G. hirsutum L.) are prized for their combination of exceptional yield, other agronomic traits, and good fiber properties, whereas the other cultivated 52-chromosome species, G. barbadense L. [2n?=?52, genomic formula?2(AD)₂], is widely regarded as having the opposite attributes. It has exceptionally good fiber qualities, but generally lower yield and less desirable agronomic traits. Breeders have long aspired to combine the best attributes of G. hirsutum and G. barbadense, but have had limited success. F₁ hybrids are readily created and largely fertile, so the limited success may be due to cryptic biological and technical challenges associated with the conventional methods of interspecific introgression. We have developed a complementary alternative approach for introgression based on chromosome substitution line, followed by increasingly sophisticated genetic analyses of chromosome-derived families to describe the inheritance and breeding values of the chromosome substitution lines. Here, we analyze fiber quality traits of progeny families from a partial diallel crossing scheme among selected chromosome substitution lines (CS-B lines). The results provide a more detailed and precise QTL dissection of fiber traits, and an opportunity to examine allelic interaction effects between two substituted chromosomes versus one substituted chromosome. This approach creates new germplasm based on pair wise combinations of quasi-isogenic chromosome substitutions. The relative genetic simplicity of two-chromosome interactions departs significantly from complex or RIL-based populations, in which huge numbers of loci are segregating in all 26 chromosome pairs. Data were analyzed according to the ADAA genetic model, which revealed significant additive, dominance, and additive-by-additive epistasis effects on all of the fiber quality traits associated with the substituted chromosome or chromosome arm of CS-B lines. Fiber of line 3-79, the donor parent for the substituted chromosomes, had the highest Upper Half Mean length (UHM), uniformity ratio, strength, elongation, and lowest micronaire among all parents and hybrids. CS-B16 and CS-B25 had significant additive effects for all fiber traits. Assuming a uniform genetic background of the CS-B lines, the comparative analysis of the double-heterozygous hybrid combinations (CS-B?×?CS-B) versus their respective single heterozygous combinations (CS-B?×?TM-1) demonstrated that interspecific epistatic effects between the genes in the chromosomes played a major role in most of the fiber quality traits. Results showed that fiber of several hybrids including CS-B16?×?CS-B22Lo, CS-B16?×?CS-B25 and CS-B16?×?TM-1 had significantly greater dominance effects for elongation and hybrid CS-B16?×?CS-B17 had higher fiber strength than their parental lines. Multiple antagonistic genetic effects were also present for fiber quality traits associated with most of the substituted chromosomes and chromosome arms. Results from this study highlight the vital importance of epistasis in fiber quality traits and detected novel effects of some cryptic beneficial alleles affecting fiber quality on the 3-79 chromosomes, whose effects were not detected in the 3-79 parental lines.     

An additive-dominance model to determine chromosomal effects in chromosome substitution lines and other gemplasms

When using chromosome substitution (CS) lines in a crop breeding improvement program, one needs to separate the effects of the substituted chromosome from the remaining chromosomes. This cannot be done with the traditional additive-dominance (AD) model where CS lines, recurrent parent, and their hybrids are used. In this study, we develop a new genetic model and software, called a modified AD model with genotype × environment interactions, which can predict additive and dominance genetic effects attributed to a substituted alien chromosome in a CS line as well as the overall genetic effects of the non-substituted chromosomes. In addition, this model will predict the additive and dominance effects of the same chromosome of interest (i.e. chromosome 25 of cotton in this study) in an inbred line, as well as the effects of the remaining chromosomes in the inbred line. The model requires a CS line, its recurrent parent and their F₁ and/or F₂ hybrids between the substitution lines and several inbred lines. Monte Carlo simulation results showed that genetic variance components were estimated with no or slight bias when we considered this modified AD model as random. The correlation coefficient between predicted effects and true effects due to the chromosomes of interest varied from zero to greater than 0.90 and it was positively relative to the difference between the CS line and the recurrent line. To illustrate the use of this new genetic model, an upland cotton, Gossypium hirsusum L, CS line (CS-B25), TM-1 (the recurrent parent), five elite cultivars, and the F₂ hybrids from test-crossing these two lines with the five elite cultivars were grown in two environments in Mississippi. Agronomic and fiber data were collected and analyzed. The results showed that the CS line, CS-B25, which has chromosome 25 from line 3 to 79, Gossypium barbadense substituted into TM-1, had positive genetic associations with several fiber traits. We also determined that Chromosome 25 from FiberMax 966 had significantly positive associations with fiber length and strength; whereas, chromosome 25 from TM-1 and SureGrow 747 had detectable negative genetic effects on fiber strength. The new model will be useful to determine effects of the chromosomes of interest in various inbred lines in any diploid or amphidiploid crop for which CS lines are available.     

Mapping quantitative trait loci for lint yield and fiber quality across environments in a Gossypium hirsutum × Gossypium barbadense backcross inbred line population

Identification of stable quantitative trait loci (QTLs) across different environments and mapping populations is a prerequisite for marker-assisted selection (MAS) for cotton yield and fiber quality. To construct a genetic linkage map and to identify QTLs for fiber quality and yield traits, a backcross inbred line (BIL) population of 146 lines was developed from a cross between Upland cotton (Gossypium hirsutum) and Egyptian cotton (Gossypium barbadense) through two generations of backcrossing using Upland cotton as the recurrent parent followed by four generations of self pollination. The BIL population together with its two parents was tested in five environments representing three major cotton production regions in China. The genetic map spanned a total genetic distance of 2,895 cM and contained 392 polymorphic SSR loci with an average genetic distance of 7.4 cM per marker. A total of 67 QTLs including 28 for fiber quality and 39 for yield and its components were detected on 23 chromosomes, each of which explained 6.65–25.27 % of the phenotypic variation. Twenty-nine QTLs were located on the At subgenome originated from a cultivated diploid cotton, while 38 were on the Dt subgenome from an ancestor that does not produce spinnable fibers. Of the eight common QTLs (12 %) detected in more than two environments, two were for fiber quality traits including one for fiber strength and one for uniformity, and six for yield and its components including three for lint yield, one for seedcotton yield, one for lint percentage and one for boll weight. QTL clusters for the same traits or different traits were also identified. This research represents one of the first reports using a permanent advanced backcross inbred population of an interspecific hybrid population to identify QTLs for fiber quality and yield traits in cotton across diverse environments. It provides useful information for transferring desirable genes from G. barbadense to G. hirsutum using MAS.     

Effects of chromosome-specific introgression in upland cotton on fiber and agronomic traits

Interspecific chromosome substitution is among the most powerful means of introgression and steps toward quantitative trait locus (QTL) identification. By reducing the genetic "noise" from other chromosomes, it greatly empowers the detection of genetic effects by specific chromosomes on quantitative traits. Here, we report on such results for 14 cotton lines (CS-B) with specific chromosomes or chromosome arms from G. barbadense L. substituted into G. hirsutum and chromosome-specific F2 families. Boll size, lint percentage, micronaire, 2.5% span length, elongation, strength, and yield were measured by replicated field experiments in five diverse environments and analyzed under an additive-dominance (AD) genetic model with genotype and environment interaction. Additive effects were significant for all traits and dominance effects were significant for all traits except 2.5% span length. CS-B25 had additive effects increasing fiber strength and fiber length and decreasing micronaire. CS-B16 and CS-B18 had additive effects related to reduced yields. The results point toward specific chromosomes of G. barbadense 3-79 as the probable locations of the genes that significantly affect quantitative traits of importance. Our results provided a scope to analyze individual chromosomes of the genome in homozygous and heterozygous conditions and thus detected novel effects of alleles controlling important QTL.     

Genetic effects of individual chromosomes in cotton cultivars detected by using chromosome substitution lines as genetic probes

Determination of chromosomes or chromosome arms with desirable genes in different inbred lines and/or crosses should provide useful genetic information for crop improvement. In this study, we applied a modified additive-dominance model to analyze a data set of 13 cotton chromosome substitution lines and their recurrent parent TM-1, five commercial cultivars, and their 70 F(2) hybrids. The chromosome additive and dominance variance components for eight agronomic and fiber traits were determined. On average, each chromosome or chromosome arm was associated with 6.5 traits in terms of additive and/or dominance effects. The chromosomes or chromosome arms, which contributed significant additive variances for the traits investigated, included 2, 16, 18, 25, 5sh (short arm), 14sh, 15sh, 22sh, and 22Lo (long arm). Chromosome additive effects were also predicted in this study. The results showed that CS-B 25 was favorably associated with several fiber traits, while FM966 was favorably associated with both yield and fiber traits with alleles on multiple chromosomes or chromosome arms. Thus, this study should provide valuable genetic information on pure line development for several improved traits such as yield and fiber quality.     

SSR marker-assisted improvement of fiber qualities in Gossypium hirsutum using G. barbadense introgression lines

Key message

This study demonstrates the first practical use of CSILs for the transfer of fiber quality QTLs into Upland cotton cultivars using SSR markers without detrimentally affecting desirable agronomic characteristics.

Abstract

Gossypium hirsutum is characterized by its high lint production and medium fiber quality compared to extra-long staple cotton G. barbadense. Transferring valuable traits or genes from G. barbadense into G. hirsutum is a promising but challenging approach through a traditional interspecific introgression strategy. We developed one set of chromosome segment introgression lines (CSILs), where TM-1, the genetic standard in G. hirsutum, was used as the recipient parent and the long staple cotton G. barbadense cv. Hai7124 was used as the donor parent by molecular marker-assisted selection (MAS). Among them, four CSILs, IL040-A4-1, IL080-D6-1, IL088-A7-3 and IL019-A2-6, found to be associated with superior fiber qualities including fiber length, strength and fineness QTL in Xinjiang were selected and backcrossed, and transferred these QTLs into three commercial Upland cotton cultivars such as Xinluzao (XLZ) 26, 41 and 42 grown in Xinjiang. By backcrossing and self-pollinating twice, five improved lines (3262-4, 3389-2, 3326-3, 3380-4 and 3426-5) were developed by MAS of background and introgressed segments. In diverse field trials, these QTLs consistently and significantly offered additive effects on the target phenotype. Furthermore, we also pyramided two segments from different CSILs (IL080-D6-1 and IL019-A2-6) into cultivar 0768 to accelerate breeding process purposefully with MAS. The improved lines pyramided by these two introgressed segments showed significant additive epistatic effects in four separate field trials. No significant alteration in yield components was observed in these modified lines. In summary, we first report that these CSILs have great potential to improve fiber qualities in Upland cotton MAS breeding programs.     

Genetic Analysis for F1 Yield Traits with Conditional Approach in Island Cotton (Gossypium barbadense L.)

A genetic model with additive, dominance and genotype × environment interaction effect was employed to analyze the 3-year data of F₁ hybrids from 5 × 4 diallel cross, whose parents were Island cotton and had different fruit branch types. Unconditional and conditional genetic variances were conducted for analyze genetic impacts of yield components on yield. Results of unconditional genetic variances showed that there were no additive variance of total lint yield. But conditional additive effects of total lint yield, when excluding the phenotype of boll weight, boll number at prefrost, boll number at postfrost, and lint yield at prefrost, indicated that improving the additive effects of the total lint yield was still possible. Crossing and selecting component traits with high contributive additive effects could obtain good offsprings. Yield components contributed large dominance effects to the heterosis of lint yield at prefrost and total lint yield in crosses. Yield component traits were controlled with each other. The traits having positive contributive effects could be applied to further improve target traits.     

Genetic dissection of lint yield and fiber quality traits of <Emphasis Type="Italic">G. hirsutum</Emphasis> in <Emphasis Type="Italic">G. barbadense</Emphasis> background

Gossypium hirsutum L. is a widely cultivated species characterized by its high yield and wide environmental adaptability, while Gossypium barbadense is well known for its superior fiber quality. In the present report, we, for the first time, developed G. hirsutum chromosome segment introgression lines (ILs) in a G. barbadense background (GhILs_Gb) and genetically dissected the inheritance of lint yield and fiber quality of G. hirsutum in G. barbadense background. The GhILs_Gb contains introgressed segments spanning 4121.20 cM, which represents 82.20% of the tetraploid cotton genome, with an average length of 18.65 cM. A total of 39 quantitative trait loci (QTLs) for six traits are identified in this IL population planted in Xinjiang. Four QTL clusters are detected. Of them, however, three clusters have deleterious effects on fiber length and strength and boll weight, and only one cluster on Chr. D9 can be used in marker-assisted selection (MAS) to increase lint percentage and decrease micronaire value in G. barbadense. QTL mapping showed that most of yield-related QTLs detected have positive effects and increase lint yield in G. barbadense, while most of fiber quality-related QTLs have deleterious effects except for micronaire. It suggested that G. hirsutum evolved to have a high lint yield. Several lines improved in lint percentage and boll size in G. barbadense by introgressed one fragment of G. hirsutum have been developed from the GhILs_Gb. The ILs developed, and the analyses presented here will enhance the understanding of the genetics of lint yield and fiber quality in G. hirsutum and facilitate further molecular breeding to improve lint yield in G. barbadense.     

海岛棉F1产量性状的条件遗传分析

调查了海岛棉5×4不完全双列杂交实验的3年产量性状资料,运用包括加性、显性、加性×环境互作、显性×环境互作的遗传模型进行条件和非条件的遗传分析.双列杂交的亲本具有不同果枝类型.非条件遗传方差结果表明,总皮棉产量没有检测到显著的非条件加性效应方差.但是铃重、霜前铃数、霜后铃数以及霜前皮棉产量的条件分析结果发现这些性状的加性效应均对总皮棉产量的加性效应有贡献.因此,可通过这些性状改良总皮棉产量的加性效应表现.当某材料产量构成因素的加性贡献率比较高时,选择该材料作为杂交亲本可望获得具有较好总皮棉产量表现的后代.各产量构成因素的显性效应对霜前皮棉产量和总皮棉产量的杂种优势具有较大的贡献率.产量构成因素之间又相互影响.那些能够检测到显著的正向贡献率的性状将为进一步改良目标性状提供可能.本研究结果显示运用条件分析方法不仅能分析原因性状对目标性状的贡献率,还可以分析特定亲本(或组合)的某一性状对该亲本或组合目标性状的作用大小和正负,据此就可以指导某一亲本后代或组合的目标性状的间接选择.这对实际育种中具体组合的选择具有重要的意义.     

Breeding Potential of Introgression Lines Developed from Interspecific Crossing between Upland Cotton (Gossypium hirsutum) and Gossypium barbadense: Heterosis,Combining Ability and Genetic Effects

Upland cotton (Gossypium hirstum L.), which produces more than 95% of the world natural cotton fibers, has a narrow genetic base which hinders progress in cotton breeding. Introducing germplasm from exotic sources especially from another cultivated tetraploid G. barbadense L. can broaden the genetic base of Upland cotton. However, the breeding potential of introgression lines (ILs) in Upland cotton with G. barbadense germplasm integration has not been well addressed. This study involved six ILs developed from an interspecific crossing and backcrossing between Upland cotton and G. barbadense and represented one of the first studies to investigate breeding potentials of a set of ILs using a full diallel analysis. High mid-parent heterosis was detected in several hybrids between ILs and a commercial cultivar, which also out-yielded the high-yielding cultivar parent in F₁, F₂ and F₃ generations. A further analysis indicated that general ability (GCA) variance was predominant for all the traits, while specific combining ability (SCA) variance was either non-existent or much lower than GCA. The estimated GCA effects and predicted additive effects for parents in each trait were positively correlated (at P<0.01). Furthermore, GCA and additive effects for each trait were also positively correlated among generations (at P<0.05), suggesting that F₂ and F₃ generations can be used as a proxy to F₁ in analyzing combining abilities and estimating genetic parameters. In addition, differences between reciprocal crosses in F₁ and F₂ were not significant for yield, yield components and fiber quality traits. But maternal effects appeared to be present for seed oil and protein contents in F₃. This study identified introgression lines as good general combiners for yield and fiber quality improvement and hybrids with high heterotic vigor in yield, and therefore provided useful information for further utilization of introgression lines in cotton breeding.     

Association Mapping for Epistasis and Environmental Interaction of Yield Traits in 323 Cotton Cultivars under 9 Different Environments

Improving yield is a major objective for cotton breeding schemes, and lint yield and its three component traits (boll number, boll weight and lint percentage) are complex traits controlled by multiple genes and various environments. Association mapping was performed to detect markers associated with these four traits using 651 simple sequence repeats (SSRs). A mixed linear model including epistasis and environmental interaction was used to screen the loci associated with these four yield traits by 323 accessions of Gossypium hirsutum L. evaluated in nine different environments. 251 significant loci were detected to be associated with lint yield and its three components, including 69 loci with individual effects and all involved in epistasis interactions. These significant loci explain ∼ 62.05% of the phenotypic variance (ranging from 49.06% ∼ 72.29% for these four traits). It was indicated by high contribution of environmental interaction to the phenotypic variance for lint yield and boll numbers, that genetic effects of SSR loci were susceptible to environment factors. Shared loci were also observed among these four traits, which may be used for simultaneous improvement in cotton breeding for yield traits. Furthermore, consistent and elite loci were screened with −Log₁₀ (P-value) >8.0 based on predicted effects of loci detected in different environments. There was one locus and 6 pairs of epistasis for lint yield, 4 loci and 10 epistasis for boll number, 15 loci and 2 epistasis for boll weight, and 2 loci and 5 epistasis for lint percentage, respectively. These results provided insights into the genetic basis of lint yield and its components and may be useful for marker-assisted breeding to improve cotton production.     

Genetic changes in plant growth and their associations with chromosomes from <Emphasis Type="Italic">Gossypium barbadense</Emphasis> L. in <Emphasis Type="Italic">G. hirsutum</Emphasis> L

Cotton (Gossypium spp.) plant growth is an important time-specific agronomic character that supports the development of squares, flowers, boll retention, and yield. With the use of a mixed linear model approach, we investigated 14 cotton chromosome substitution (CS-B) lines and their chromosome-specific F₂ hybrids for genetic changes in plant growth that was measured during the primary flowering time under two environments. The changes in additive and dominance variances for plant height and number of mainstem nodes are reported, showing that additive effects for these two traits were a key genetic component after initial flowering occurred in the field. Time-specific genetic variance components were also detected where phenotypic values observed at time t were conditioned on the events occurring at time t − 1, demonstrating new genetic variations arising at several time intervals during plant growth. Results also revealed that plant height and number of nodes shared some common influence due to additive effects during plant development. With the comparative analyzes, chromosomes associated with the genetic changes in plant growth were detected. Therefore, these results should add new understanding of the genetics underlying these time-specific traits. Mention of trademark or proprietary product does not constitute a guarantee or warranty of the product by the United States Department of Agriculture and does not imply its approval to the exclusion of other products that may also be suitable.     

陆地棉产量性状QTLs的分子标记及定位

用我国的高产栽培品种泗棉3号和美国栽培品种TM-1为材料,构建F₂和F_2∶3作图群体,应用301对SSR引物和1040个RAPD引物,对产量性状QTLs进行了分子标记筛选,结果共筛选出了37对SSR多态性引物和10个RAPD多态性引物的49个位点,鉴定出了控制产量性状变异的主效QTLs。定位于第9染色体的连锁群,分别具有控制铃重、衣分和籽指的主效QTLs,铃重的2个QTLs分别解释F_2∶3群体表型变异的18.2%和21.0%;在F₂群体检测到的1个衣分QTL解释表型变异的25%,另一个衣分QTL在F₂群体和F_2∶3群体都检测到,解释F₂群体衣分的24.9%的表型变异,解释F_2∶3群体衣分的5.9%的表型变异;在F_2∶3群体铃重的一个QTL的同一位置同时检测到一个籽指QTL,它解释15.6%的表型变异,是一因多效或是紧密连锁的两个QTLs,有待进一步研究。本研究标记的产量性状主效QTLs可用于棉花产量性状的标记辅助选择。     

彩色棉种质资源农艺性状和纤维品质鉴定与分析

基于农艺性状和纤维品质对61份彩色棉种质材料进行鉴定分析,结果表明：材料间衣分、2．5％跨长、马克隆值呈极显著差异,整齐度、伸长率、比强度和单株铃数存在显著差异,株高、果枝数、单铃重差异不显著;供试材料纤维品质较差,除中国农业科学院棉花研究所选育的棕125、棕絮1号等材料外,大部分种质系2．5％跨长、比强度等指标不能满足纺织工业的需求,但仍有31份种质系单一性状较优,如棕2—63（IAA）、棕3-944等。采用类平均法对供试材料进行聚类分析,61份材料聚为7个类群,供试材料表现型性状相似较低,尤其部分基础彩色棉遗传材料与其他材料相似性极低,单独构成一类,如皱缩红鸡角叶棕絮、hunan绿等。综合分析表明,供试材料农艺性状和纤维品质较差,遗传多样性较丰富。     

Inheritance of long staple fiber quality traits of Gossypium barbadense in G. hirsutum background using CSILs

Gossypium hirsutum is a high yield cotton species that exhibits only moderate performance in fiber qualities. A promising but challenging approach to improving its phenotypes is interspecific introgression, the transfer of valuable traits or genes from the germplasm of another species such as G. barbadense, an important cultivated extra long staple cotton species. One set of chromosome segment introgression lines (CSILs) was developed, where TM-1, the genetic standard in G. hirsutum, was used as the recipient parent and the long staple cotton G. barbadense Hai7124 was used as the donor parent by molecular marker-assisted selection (MAS) in BC₅S_1–4 and BC₄S_1–3 generations. After four rounds of MAS, the CSIL population was comprised of 174 lines containing 298 introgressed segments, of which 86 (49.4%) lines had single introgressed segments. The total introgressed segment length covered 2,948.7 cM with an average length of 16.7 cM and represented 83.3% of tetraploid cotton genome. The CSILs were highly varied in major fiber qualities. By integrated analysis of data collected in four environments, a total of 43 additive quantitative trait loci (QTL) and six epistatic QTL associated with fiber qualities were detected by QTL IciMapping 3.0 and multi-QTL joint analysis. Six stable QTL were detected in various environments. The CSILs developed and the analyses presented here will enhance the understanding of the genetics of fiber qualities in long staple G. barbadense and facilitate further molecular breeding to improve fiber quality in Upland cotton.     

数量性状的核质互作遗传效应分析:二倍体植株遗传模型

提出了能分析二倍体植株数量性状核质互作效应的遗传模型,该模型把控制数量性状总的遗传效应分为核效应、质效应和核质互作效应,以及它们分别与环境作用的效应。其中,核质互作效应可进一步分解为加性核质互作与显性核质互作。基于平衡与非平衡两种双列杂交试验设计,蒙特卡罗模拟结果表明:采用混合线性模型方法进行统计分析,可以有效地估计各项遗传效应值及其方差分量。此外,运用该模型对棉花的4个数量性状(单株铃数、衣分、2.5%跨长和麦克隆值)进行了遗传分析。     

Resequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement

Upland cotton (Gossypium hirsutum) is the world's largest source of natural fibre and dominates the global textile industry. Hybrid cotton varieties exhibit strong heterosis that confers high fibre yields, yet the genome‐wide effects of artificial selection that have influenced Upland cotton during its breeding history are poorly understood. Here, we resequenced Upland cotton genomes and constructed a variation map of an intact breeding pedigree comprising seven elite and 19 backbone parents. Compared to wild accessions, the 26 pedigree accessions underwent strong artificial selection during domestication that has resulted in reduced genetic diversity but stronger linkage disequilibrium and higher extents of selective sweeps. In contrast to the backbone parents, the elite parents have acquired significantly improved agronomic traits, with an especially pronounced increase in the lint percentage. Notably, identify by descent (IBD) tracking revealed that the elite parents inherited abundant beneficial trait segments and loci from the backbone parents and our combined analyses led to the identification of a core genomic segment which was inherited in the elite lines from the parents Zhong 7263 and Ejing 1 and that was strongly associated with lint percentage. Additionally, SNP correlation analysis of this core segment showed that a non‐synonymous SNP (A‐to‐G) site in a gene encoding the cell wall‐associated receptor‐like kinase 3 (GhWAKL3) protein was highly correlated with increased lint percentage. Our results substantially increase the valuable genomics resources available for future genetic and functional genomics studies of cotton and reveal insights that will facilitate yield increases in the molecular breeding of cotton.     

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.