Assessing the breeding potential of day-neutral converted racestock germplasm in the Pee Dee cotton germplasm enhancement program

The primitive, upland cotton landrace collection represents one of the untapped genetic resources in cotton breeding programs. Efforts to utilize these resources have been slow, but the development of day-neutral converted germplasm lines offers tremendous potential for broadening the genetic base in upland cotton. Using topcross hybrids involving elite germplasm from the unique Pee Dee germplasm enhancement program, we evaluated the breeding potential of a select number of day-neutral converted racestocks. The mean performance of parental lines and F₂ topcross hybrids along with genetic effect estimates indicate that day-neutral converted germplasm lines decreased agronomic performance while increasing fiber quality performance. Results suggest that crosses between day-neutral converted racestocks and elite Pee Dee germplasm lines result in new allelic combinations associated with improved fiber quality performance that interact in a non-additive way. However, it appears that converted racestocks transmit negatively correlated alleles for agronomic performance and fiber quality. These negatively correlated allelic combinations present a major challenge for cotton breeding programs. Future efforts that incorporate DNA based selection methods to identify and fix introgressed segments from converted racestocks and their offspring should enhance the use of the genetic variation present in the primitive racestock germplasm accessions.     

AFLP marker associations with agronomic and fiber traits in cotton

DNA markers linked with major QTL contributing to traits of importance will be a useful tool for cotton (Gossypium spp.) genetics and breeding. We crossed four photoperiod-sensitive accessions of cotton, G. hirsutum L., with a cultivar, selected day-neutral plants and backcrossed four times to each of the four photoperiod-sensitive accessions, selecting day-neutral plants at each generation. The day-neutral plants from the first cross and the four backcross generations were advanced to the F₆. These 20 day-neutral lines and four cultivars were grown in two environments at Mississippi State, MS and scored for seven agronomic and fiber quality traits. They were also scored for AFLP markers using a bulk sample of leaves from each of 24 lines. More than 50 AFLP markers were associated with the seven traits with fewer markers associated with fiber than agronomic traits. However, one to four markers were associated with 22–93% of the phenotypic variability of each of the seven traits. The results suggest that selected markers could be used in marker assisted selection (MAS) in crosses designed to use alleles from exotic accessions or cultivars to develop elite breeding lines for cotton improvement.     

利用棉花纤维品质相关QTL评价海陆渐渗品种品质初探

 选用第7、13、25号染色体上纤维品质相关QTL(Quantitative trait locus)密集分布区间的48对SSR（Simple sequence repeat）引物,对48份棉花种质进行多态性检测,研究结果显示在实验材料中3对SSR引物具有陆海差异多态性,相关分析表明3个优质基因SSR位点与纤维长度和纤维强度达到极显著相关。通过与海岛棉带型比对、追踪,从分子水平上明确了这些品种中来源于海岛棉渐渗于陆地棉的优异基因区段,为下一步分子标记辅助聚合育种提供了理论参考。     

Performance and combining ability in cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis> L.) populations with diverse parents

Improving fiber quality properties of cotton is important for increasing the efficiency of manufacturing textiles, including enhancing yarn quality and spinning performance. This study was conducted to determine if we could identify valuable cotton cultivars to use as parents in breeding programs with the goal of improving fiber properties. Seven parents were combined in a diallel design and selfed to obtain 21 F₂ populations. Positive general and specific combining ability effects were observed for all traits. General combining ability tended to be larger than specific combining ability, indicating these traits are controlled primarily by additive genetic effects. Correlations among traits were generally positive except for lint yield correlations with fiber strength and length. For improving the fiber quality measures of strength and length, line 7235 shows excellent general combining ability effects. SG125 would provide elite germplasm to increase agronomic measures of lint yield and lint percent. The MD51 genotype has the highest potential among the genotypes tested here to provide germplasm combining both improved yield and fiber strength. These parents, or their selected progeny, should be useful in a breeding program to generate variability from which selection can be used to identify lines with improved fiber and/or agronomic properties.     

Targeted identification of association between cotton fiber quality traits and microsatellite markers

Primitive and exotic accessions of cotton are potential sources of favorable alleles for genetic improvement, enriching diversity in the genetically constricted gene pool of elite cultivars. Three exotic accessions of cotton (MDN101, MDN063 and MDN257), collected from different parts of Central America and converted to day-neutral flowering; and four elite cultivars (PD94042, DES56, PMHS200 and Acala Maxxa) representing the US cotton gene pool were used as parents to create experimental populations. The corresponding F₂ and F_2:3 progenies of these populations were grown in two successive years (i.e., some in 2011–2012, some in 2012–2013) and phenotypes were scored in both F₂ and F_2:3 progenies in all 3 years (2011–2012–2013). These populations were screened with 113 polymorphic microsatellite markers selected from “hotspots” for fiber quality quantitative trait loci in the cotton genome and single marker analyses were performed to identify significant associations of the markers with six fiber quality traits. A total of 134 nominal marker-trait associations were identified, among which 15 were significant after Bonferroni correction for multiple comparisons. In 67 of 134 nominal associations and 4 of 15 significant associations, the exotic parents contributed favorable alleles to multiple backgrounds and for multiple traits, in addition to the traits for which they were selected. These results indicate that utilization of exotic and wild accessions of cotton is useful in introducing favorable alleles into the cultivated cotton gene pool for genetic improvement.     

Genetic diversity in red clover (Trifolium pratense L.) revealed by morphological and microsatellite (SSR) markers

The NPGS-USDA core collection with 85 accessions of red clover, an important forage species, is little described. The goal of the present study was to evaluate the diversity of a set of accessions from the core collection at the morphological and molecular level in order to extract some valuable accessions for Brazilian red clover breeding programs. Twenty-one morphological traits, collected in field and greenhouse in South Brazil, and seven SSR markers were used to describe 57 accessions from the U.S. core collection and one population cultivated in Southern Brazil. Variation between accessions was large for most of the 21 morphological traits. A cluster analysis based on the morphological traits revealed five distinct clusters that separated the populations according to flowering earliness, as already described, but also according to persistency, growth habit and dry matter productivity. Over seven SSR loci, the number of alleles averaged 11.1 alleles per locus. Genetic diversity measured with SSR markers was high, with a mean expected heterozygosity of 0.86. An analysis of molecular variance revealed that the largest proportion of variation (83.6%) resided at the within population level. Although the molecular markers also separated accessions into five clusters, there was no coincidence between the composition of groups found with morphological and molecular data. Use of genetic diversity in breeding programs requires to use the most promising populations, to combine positive traits such as persistency and forage yield, and probably to use within population variation to detect valuable genotypes that could be used as parents of synthetic varieties.     

Mining Elite Sea-Island Cotton Germplasm Based on Phenotyping and SSR Markers

[Objective] An elite germplasm resource of sea-island cotton with outstanding traits was mined in order to accelerate the breeding process of new varieties. [Method] The core collections of sea-island cotton germplasm consisted of 178 accessions were used as experimental materials in this study. Analyses of variability and diversity were performed through detecting phenotypic data of six main breeding-targeted traits, including boll weight, boll number per plant, lint percentage, fiber length, fiber strength, and micronaire. The elite germplasm of sea-island cotton was selected according to 10% optimal sampling strategy based on the phenotypic value of each trait. The 120 pairs of polymorphic simple sequence repeat (SSR) primers were used to analyze the polymorphism of 178 accessions of the core collections. Then, we conducted the population structure and clustering analysis based on the genotyping results. According to the results of cluster analysis, the primary elite germplasm was further selected, and the final elite germplasm of sea-island cotton was identified. [Result] The results showed that there was a high variability and abundant genetic diversity in the 6 studied traits. In 178 accessions of sea-island cotton, 262 alleles were detected by 120 pairs of SSR primers, with an average of 2.18 loci. The average polymorphism information content (PIC) was 0.067 8-0.630 0, with an average of 0.296 0, showing moderate polymorphism. The cluster analysis showed that the core collection of sea-island cotton was divided into six groups. twenty-three elite germplasm resources of sea-island cotton were identified based on phenotypic value and cluster analysis of SSR markers. [Conclusion] The germplasm of sea-island cotton can be analyzed and evaluated based on the phenotyping and SSR markers, and then the elite germplasm of sea-island cotton can be identified. These results provided the material basis for the genetic breeding of sea-island cotton, as well as the important reference and basis for the mining and identification of crop elite germplasm.     

Genetic association of cotton yield with its component traits in derived primitive accessions crossed by elite upland cultivars using the conditional ADAA genetic model

Boll number, lint percentage, and boll weight are three component traits for lint yield of upland cotton, Gossypium hirsutum L. Selecting high yielding lines or hybrids depends on the ability to dissect the genetic relationship of lint yield with these component traits. In this study, 14 day-neutral lines with desirable fiber quality derived from primitive accessions were top crossed with five commercial cultivars. The F₂ populations and parents were grown in one location in 1998 and two locations in 1999 at Mississippi State, MS. The F₃ populations and parents were grown in two locations in 2000. Lint yield and three component traits were measured and analyzed by the ADAA genetic model with the mixed model based conditional approach. Results showed that boll number or boll number with lint percentage or boll weight contributed to the majority of the phenotypic variance and variance components for lint yield. Boll number was more important than the other two component traits in terms of various genetic effects. The results also showed that the combination of boll number and boll weight greatly increased the contribution to lint yield even though boll weight itself had no significant contribution to lint yield compared to boll number alone. The genetic contribution effects were also predicted due to single component traits or their combinations for parents and crosses. The results revealed that the balanced selection of boll weight and boll number should be considered to obtain high yielding hybrids or pure lines. Contribution of the USDA-ARS in cooperation with the Mississippi Agric. and Forestry Exp. Stn. Mention of trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by USDA, ARS and does not imply its approval to the exclusion of other products or vendors that may also be suitable.     

Genetic effects and genetic values of fiber properties in F2 and F3 hybrids between germplasm lines and high yield cultivars

Utilization of cotton (Gossypium hirsutum L.) germplasm for genetic improvement of fiber properties requires determination of genetic effects in the germplasm lines. A study was designed to analyze genetic populations derived from multiple crosses between nine germplasm lines as male parents and five cultivars and elite breeding lines as female parents to determine genetic values of fiber properties. Parents and F₂ populations were planted at 2 field sites in 2010 and 2011 with 4 and 3 replicates, respectively, and parents and F₃ populations were planted at 2 field sites in 2011 with 3 replicates. Lint yield and seven fiber properties were analyzed by an additive and dominant model with genotype by environment interaction effects. Significant additive and dominant effects were identified for both lint yield and fiber properties. Germplasm lines JC60, JC65, JC186, and SP205 were good general combiners for micronaire, elongation, strength, 50 % span length, short fiber content, and fineness. Six to fifteen crosses were detected with favorable heterozygous dominant effects for lint yield and diverse fiber traits, which suggest useful heterosis of these hybrids. Favorable additive correlations were identified between fiber properties such as micronaire versus 50 % span length (?0.57), micronaire versus fineness (0.82), strength versus 50 % span length (0.54), strength versus short fiber content (?0.69), and 50 % span length versus short fiber content (?0.78) while unfavorable additive correlations were not identified among fiber properties. These results indicated potential of simultaneous genetic improvement for these multiple properties in breeding populations derived from these germplasm lines.     

海岛棉遗传多样性的SRAP标记分析

利用SRAP标记, 选用132对带型清晰的多态性引物, 对我国引入海岛棉以来培育的36个国内品种及20个国外品种进行遗传多样性分析。共检测到419个多态性位点, 每组合的多态性条带数从2~9不等, 平均为3.17。利用NTSYS-pc 2.10e 软件采用Jaccard’s相似系数和UPGMA方法进行聚类分析。结果表明, 大部分具有亲缘关系的品种聚在同类中, 说明其结果与系谱具有一定的相符性; 56个品种的平均遗传相似系数为0.497, 变化范围在0.312~0.876之间, 说明我国海岛棉品种在分子水平上存在较大差异; 我国3个育种时期育成品种的平均相似系数依次为0.501、0.507和0.548, 表明我国现在育成的品种相对于早期品种遗传多样性在逐渐降低。这些结果为我国海岛棉育种提供了有益的参考。     

Seed trait evaluation of <Emphasis Type="Italic">Gossypium barbadense</Emphasis> L. chromosomes/arms in a <Emphasis Type="Italic">G. hirsutum</Emphasis> L. background

Investigation of cotton nutritional components is important because its seeds provide a useful nutritional profile and can possibly serve as a biofuel resource. In this study, five cultivars, 13 cotton chromosome substitution (CS-B) lines, their donor parent, '3-79', and their recurrent parent, 'TM-1', were evaluated for seed traits over four environments. A mixed linear model approach with the jackknife method was employed to estimate variance components and to predict genotypic effects for each seed trait. Genotypic effects were more important than genotype by environment interaction for all seed traits. Chromosome associations with these seed traits were detected using the comparative method by comparing the differences between each CS-B line and TM-1. For example, chromosome 4 of 3-79 in TM-1 background was associated with reduced seed index (SI), embryo percentage, protein percentage while associated with increased seed oil percentage and seed fiber percentage. Other chromosome associations with these seed traits were also observed in this study. SI was highly correlated with three seed index traits: seed protein index, seed oil index (OI), and seed fiber index. Lint percentage, boll number, and lint yield were positively correlated with protein percentage while negatively correlated with SI and OI. SI and seed fiber content exhibited negative correlations with micronaire but positive correlations with fiber length and strength. Results suggested that agronomic traits and seed nutrition components can be improved simultaneously.     

Evaluation of genetic variances, heritabilities, and correlations for yield and fiber traits among cotton F2 hybrid populations

Summary F₂ hybrid cultivars continue to occupy a small portion of the cotton (Gossypium hirsutum L.) production are in the United States, but occupy a larger proportion of the production area in some other countries. Sixty-four F₂ hybrids resulting from crosses of four commercial cultivars and 16 pest-resistant germplasm lines were evaluated for five fiber and four yield traits in four environments at Mississippi State, MS. An additive-dominance genetic model was employed for these traits. The minimum norm quadratic unbiased estimation (MINQUE) method was used with a mixed model approach for estimating genetic variance and covariance components and for predicting genetic correlations. This study investigated genetic variances, heritabilities, and genetic and phenotypic correlations between agronomic and fiber traits among these 64 F₂ hybrid populations and discussed the usefulness of these populations for use as hybrids or for selections for pure lines.Dominance variance accounted for the major proportion of the phenotypic variances for lint yield, lint percentage, and boll size indicating that hybrids should have an advantage for these traits compared to pure lines. A low proportion of additive variance for fiber traits and the significant additive x environment variance components indicated a lack of substantial useful additive genetic variability for fiber traits. This suggests that selections for pure lines within these F₂ populations would have limited success in improving fiber traits. Genetic and phenotypic correlation coefficients were of comparable magnitude for most pairs of characters. Fiber strength showed a positive additive genetic correlation with boll weight. Dominance genetic correlations of fiber strength with elongation and 2.5% span length were also significant and positive; however, the additive genetic correlation of length and strength was zero.Contribution of the USDA-ARS in cooperation with the Mississippi Agric. and Forestry Exp. Stn.     

Genetic variance components and genetic effects among eleven diverse upland cotton lines and their F2 hybrids

Selecting high yielding upland cotton, Gossypium hirsutum L. lines with improved fiber quality is a primary breeding goal. A diverse set of ten cultivars and one breeding line were crossed in a half diallel. Parents and F₂ hybrids were grown in three environments at Mississippi State, MS. Ten agronomic and fiber traits were analyzed by a mixed linear model approach based on the additive-dominance genetic model. Variance component, genetic effects and genetic correlations were calculated. ‘Acala Ultima’ was a desirable general combiner for fiber length, uniformity, strength, micronaire, lint percentage, and boll weight. ‘FiberMax 966’ was a desirable general combiner for fiber length, uniformity, strength, and all agronomic traits. ‘Tamcot Pyramid’ and M240 were poor general combiners for both fiber and agronomic traits. ‘Coker 315’ was a good general combiner for fiber length, uniformity, micronaire, boll weight, boll number, and yield. Heterozygous dominance effects were associated with several crosses, which suggest their use as hybrids.     

Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of upland cotton

Genetic mapping is an essential tool for cotton (Gossypium hirsutum L.) molecular breeding and application of DNA markers for cotton improvement. In this present study, we evaluated an RI population including 188 RI lines developed from 94 F₂-derived families and their two parental lines, ‘HS 46’ and ‘MARCABUCAG8US-1-88’, at Mississippi State, MS, for two years. Fourteen agronomic and fiber traits were measured. One hundred forty one (141) polymorphic SSR markers were screened for this population and 125 markers were used to construct a linkage map. Twenty six linkage groups were constructed, covering 125 SSR loci and 965 cM of overall map distance. Twenty four linkage groups (115 SSR loci) were assigned to specific chromosomes. Quantitative genetic analysis showed that the genotypic effects accounted for more than 20% of the phenotypic variation for all traits except fiber perimeter (18%). Fifty six QTLs (LOD > 3.0) associated with 14 agronomic and fiber traits were located on 17 chromosomes. One QTL associated with fiber elongation was located on linkage group LGU01. Nine chromosomes in sub-A genome harbored 27 QTLs with 10 associated with agronomic traits and 17 with fiber traits. Eight chromosomes in D sub-genome harbored 29 QTLs with 13 associated with agronomic traits and 16 with fiber traits. Chromosomes 3, 5, 12, 13, 14, 16, 20, and 26 harbor important QTLs for both yield and fiber quality compared to other chromosomes. Since this RI population was developed from an intraspecific cross within upland cotton, these QTLs should be useful for marker assisted selection for improving breeding efficiency in cotton line development. Paper number J1116 of the Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Mississippi State, MS 39762. Mention of trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by USDA, ARS and does not imply its approval to the exclusion of other products or vendors that may also be suitable.     

棉花IF2群体构建及其在纤维品质遗传和杂种优势研究中的应用

以陆地棉重组自交系RIL为材料,采用RIL系间随机交配的方式构建了一个含有188个组合的IF₂群体。对该群体的棉花纤维品质性状表现进行了评价,并采用A、D遗传模型对其纤维品质性状的遗传效应和杂种优势进行了分析。结果表明,陆地棉IF₂群体中5个纤维品质性状均呈现良好的正态分布,且各性状的表型平均值大多与F₁杂交种相近,具有明显的杂种优势。显性与环境的互作效应是控制棉花纤维品质遗传的主要因素,其次是基因的加性效应,环境因素对于棉花纤维品质的杂种优势表现巨大的影响,两个环境中预测到的杂种优势值具有明显的差异。IF₂群体是棉花数量性状遗传和杂种优势预测的优良研究群体。     

陆地棉种质资源抗旱性状的关联分析

干旱是导致全世界棉花严重减产、纤维品质下降的重要因素,因此获得高产、优质、耐旱的棉花新品种一直是棉花的育种目标。本研究选取217份陆地棉栽培种组成的自然群体为研究对象,采用全生育期处理组灌水量为对照组50%的干旱胁迫处理,并在处理后期对217份材料的株高、衣分、单铃重等18个性状进行2年2点的表型鉴定,干旱胁迫后,群体间响应差异明显,多个表型性状在对照和处理间表现显著差异。通过BLUP分析表型数据并计算各性状的抗旱系数;全基因组范围选取的214对多态性SSR分子标记扫描群体,共检测到393个多态性位点,基因多样性系数平均值为0.402,范围为0.072～0.631, PIC值平均为0.329,范围为0.070～0.560;群体结构分析表明,该群体可分为2个亚群。用上述SSR标记分别对18个性状的抗旱系数进行关联分析,共关联到76个极显著位点(P<0.01),表型变异解释率为2.930%～7.218%,其中共有14个标记位点能同时被2种或以上性状检测到。研究结果可为后期棉花杂交育种亲本选择及抗旱分子标记辅助育种提供理论基础及参考依据。     

渝棉1号优质纤维QTL的标记与定位

利用陆地棉遗传标准系TM-1和优质品种渝棉1号组建了(TM-1×渝棉1号) F₂和F_2:3分离群体。通过5 544对SSR引物对亲本进行筛选,获得178个多态性标记,用其中138个构建了总长为959.7 cM的遗传图谱,覆盖棉花基因组的19%。应用复合区间作图法分析了该组合的F₂单株和F₃家系纤维品质性状,共检测到12个纤维品质数量性状基因座(QTL),包括1个纤维长度的、4个纤维强度的、3个马克隆值的、3个整齐度的和1个伸长率的,分别解释各性状表型变异的6.1%、5.31%~14.62%、7.88%~19.17%、7.4%~11.71%和8.26%。研究还发现Chr.23和Chr.24是优质纤维QTLs的富集区。     

Genetic Dissection of Allelic Loci Associated with Economic Traits of Upland Cottons in Xinjiang

[Objective] We completed anassociation analysis of economic traits for upland cotton using simple sequence repeat (SSR) markers. We then explored the allelic variation sites to analyze the genetic basis of economically important traits, studied the genetic mechanism of Xinjiang upland cotton, and aimed to accelerate efficient breeding of upland cotton. [Method] We carried out polymorphic scanning on 156 upland cotton varieties in Xinjiang by screening 73 pairs of SSR markers encompassing the whole cotton genome. We constructed boxplot maps using R statistical computing software and graphics language and used TASSEL software to correlate yield or fiber quality traits with significant allelic variation loci. [Results] We obtained 10 allelic variation loci related to yield traits using the correlation analysis of Xinjiang upland cotton varieties from six different environments. The interpretation rate of phenotypic variation ranged from 6.69% to 9.88% with an average of 8.43%. Twenty-three allelic variation loci associated with fiber quality traits and phenotypic variation interpretation rates ranged from 3.73% to 13.22% with an average of 7.52%. The 22 detected quantitative trait loci were reported in previous studies and 10 showed the same associated traits as previously reported. [Conclusion] The population genetic structure of Xinjiang upland cotton varieties is simple, the linkage disequilibrium level is low, and the phenotypic traits show a stable trend under six environments. Using association analysis, we discovered unique allelic variation genes related to yield and fiber quality and diverse allele loci.     

Association analysis of fibre traits in Gossypium arboreum accessions

Advances in the use of diploid Asiatic species in cotton breeding require an understanding of the relatedness and ancestry of diploid cotton accessions, and identification of simple sequence repeat (SSR) markers associated with agronomically important phenotypic traits, for example, fibre quality. Fifty‐six Gossypium arboreum germplasm accessions introduced from nine regions of Africa, Asia and Europe were evaluated for eight fibre characters (lint percentage, lint colour, elongation, micronaire, strength, 50% span length, 2.5% span length and maturity%) and genotyped with 98 SSR markers. When viewed across all accessions most of the SSR markers were polymorphic. Population structure analysis identified six main clusters for the accessions which corresponded to different geographic regions, indicating agreement between genetic and predefined populations. The general linear model method was used to disclose marker–trait associations. Marker–trait associations were investigated by fitting single marker regression models for phenotypic traits on marker band intensities with correction for population structure. This paper illustrates the potential of association mapping in diploid cotton, because existing phenotypic data, a modest number of SSR markers, and a pioneering statistical analysis, identified interesting associations.     

棉花三系杂交种不同生态区遗传效应及优势表 现简

 选用3个核背景不同的恢复系材料和7个不同的哈克尼西棉胞质不育材料作为亲本,根据NCⅡ遗传交配设计,配置了21个杂交组合,分别在黄河流域棉区河南安阳、黄淮流域棉区河南西华和长江流域棉区安徽无为3个生态区试点种植,通过性状调查与室内考种,采用朱军的ADE模型,进行数据分析。结果表明,子棉和皮棉产量主要受到加性、显性、加性与环境互作效应的影响,衣分和铃数主要受加性、加性与环境互作效应的影响,而铃重则只受加性与环境互作效应的影响;对于纤维品质性状,纤维长度、马克隆值、比强度和整齐度受到加性效应的影响,同时,纤维长度和马克隆值还与加性与环境互作效应相关;遗传率分析与遗传方差分量分析表现一致;产量及产量性状之间有一定的遗传相关,而纤维品质性状之间的遗传相关则较小,产量和纤维品质性状之间也存在着较少的遗传相关;杂交组合的产量竞争优势表现为安阳试点>西华试点>无为试点,说明与生态环境有关。在3个不同的生态区,研究了21个杂交组合的遗传效应及优势表现,研究结果对三系杂交组合选配有一定的指导意义。