Genomic regions underlying agronomic traits in linseed （Linum usitatissimum L.） as revealed by association mapping

The extreme climate of the Canadian Prairies poses a major chal enge to improve yield. Although it is possible to breed for yield per se, focusing on yield-related traits could be advantageous because of their simpler genetic architecture. The Canadian flax core col ection of 390 accessions was genotyped with 464 simple sequence repeat markers, and phenotypic data for nine agronomic traits including yield, bol s per area, 1,000 seed weight, seeds per bol , start of flowering, end of flowering, plant height, plant branching, and lodging col ected from up to eight environments was used for association mapping. Based on a mixed model （principal component analysis （PCA） t kinship matrix （K））, 12 significant marker-trait associations for six agronomic traits were identi-fied. Most of the associations were stable across environments as revealed by multivariate analyses. Statistical simulation for five markers associated with 1000 seed weight indicated that the favorable al eles have additive effects. None of the modern cultivars carried the five favorable al eles and the maximum number of four observed in any accessions was mostly in＆amp;nbsp;breeding lines. Our results confirmed the complex genetic architecture of yield-related traits and the inherent difficulties associated with their identification while il ustrating the potential for improvement through marker-assisted selection.     

Diversity characterization and association analysis of agronomic traits in a Chinese peanut （Arachis hypogaea L.） mini-core collection

Association mapping is a powerful approach for exploring the molecular basis of phenotypic variations in plants. A peanut （Arachis hypogaea L.） mini-core collection in China comprising 298 accessions was genotyped using lo9 simple sequence repeat （SSR） markers, which identified 554 SSR alleles and phenotyped for 15 agronomic traits in three different environments, exhibiting abundant genetic and phenotypic diversity within the panel. A model-based structure analysis assigned all accessions to three groups. Most of the accessions had the relative kinship of less than o.05, indicating that there were no or weak relationships between accessions of the mini- core collection. For 15 agronomic traits in the peanut panel, generally the Q ＋ K model exhibited the best performance to eliminate the false associated positives compared to the Q model and the general linear model-simple model. In total, 89 SSR alleles were identified to be associated with 15 agronomic traits of three environments by the Q＋K model-based association analysis. Of these, eight alleles were repeatedly detected in two or three environments, and 15 alleles were commonly detected to be associated with multiple agronomic traits. Simple sequence repeat allelic effects confirmed significant differences between different genotypes of these repeatedly detected markers. Our results demonstrate the great potential of integrating the association analysis and marker-assisted breeding by utilizing the peanut mini-core collection.     

Mapping QTLs for heading synchrony in a doubled haploid population of rice in two environments

Simultaneous heading of plants within the same rice variety, also refer to heading synchrony, is an important factor that affects simultaneous ripening of the variety. Understanding of the genetic basis of heading synchrony may contribute to molecular breeding of rice with simultaneous heading and ripening. In the present study, a doubled haploid （DH） population, derived from a cross between Chunjiang 06 and TN1 was used to analyze quantitative trait locus （QTL） for heading synchrony related traits, i.e., early heading date （EHD）, late heading date （LHD）, heading asynchrony （HAS）, and tiller number （PN）. A total of 19 QTLs for four traits distributed on nine chromosomes were detected in two environments. One QTL, qHAS-8 for HAS, explained 27.7% of the phenotypic variation, co-located with the QTLs for EHD and LHD, but it was only significant under long-day conditions in Hangzhou, China. The other three QTLs, qHAS-6, qHAS-9, and qHAS-10, were identified under short-day conditions in Hainan, China, each of which explained about 11% of the phenotypic variation. Two of them, qHAS-6 and qHAS-9, were co-located with the QTLs for EHD and LHD. Two QTLs, qPN-4 and qPN-5 for PN, were detected in Hangzhou, and qPN-5 was also detected in Hainan. However, none of them was co-located with QTLs for EHD, LHD, and HAS, suggesting that PN and HAS were controlled by different genetic factors. The results of this study can be useful in marker assisted breeding for improvement of heading synchrony.     

Index selection on seed traits under direct, cytoplasmic and maternal effects in multiple environments

Crop seeds are important sources of protein, oil, and carbohydrates for food, animal feeds, and industrial products. Recently, much attention has been paid to quality and functional properties of crop seeds. However, seed traits possess some distinct genetic characteristics in comparison with plant traits, which increase the difficulty of genetically improving these traits. In this study, diallel analysis for seed models with genotype by environment interaction （GE） effect was applied to estimate the variance-covariance components of seed traits. Mixed linear model approaches were used to estimate the genetic covariances between pair-wise seed and plant traits. The breeding values （BV） were divided into two categories for the seed models. The first category of BV was defined as the combination of direct additive, cytoplasmic, and maternal additive effects, which should be utilized for selecting stable cultivars over multi-environments. The three genetic effects, together with their GE interaction, were included in the second category of BV for selecting special lines to be grown in specific ecosystems. Accordingly, two types of selection indices for seed traits, i.e., general selection index and interaction selection index, were developed and constructed on the first and the second category BV, respectively. These proposed selection indices can be applied to solve the difficult task of simultaneously improving multiple seed traits in various environments. Data of crop seeds with regard to four seed traits and four yield traits based on the modified diallel crosses in Upland cotton （Gossypium hirsutum L.） were used as an example for demonstrating the proposed methodology.     

Quantitative Trait Loci for Panicle Layer Uniformity Identified in Doubled Haploid Lines of Rice in Two Environments

Uniformity of stem height in rice directly affects crop yield potential and appearance, and has become a vital index for rice improvement. In the present study, a doubled haploid （DH） population, derived from a cross between japonica rice Chunjiang 06 and indica rice TN1 was used to analyze the quantitative trait locus （QTL） for three related traits of paniclelayer-uniformity; that is, the tallest panicle height, the lowest panicle height and panicle layer disuniforrnity in two locations：Hangzhou （HZ） and Hainan （HN）. A total of 16 QTLs for three traits distributed on eight chromosomes were detected in two different environments. Two QTLs, qTPH-4 and qTPH-8 were co-located with the QTLs for qLPH-4 and qLPH-8, which were only significant in the HZ environment, whereas the qTPH-6 and qLPH-6 located at the same interval were only significant in the HN environment. Two QTLs, qPLD-10.1 and qPLD-10.2, were closely linked to qTPH-10, and they might have been at the same locus. One QTL, qPLD-3, was detected in both environments, explaining more than 23% of the phenotypic variations. The CJ06 allele of qPLD-3 could increase the panicle layer disuniformity by 9.23 and 4.74 cm in the HZ and HN environments. Except for qPLD-3, almost all other QTLs for the same trait were detected only in one environment, indicating that these three traits were dramatically affected by environmental factors. The results may be useful for elucidation of the molecular mechanism of panicle-layer-uniformity and marker assisted breeding for super-rice.     

Constructing a high-density linkage map for Gossypium hirsutum × Gossypium barbadense and identifying QTLs for lint percentage

To introgress the good fiber quality and yield from Gossypium barbadense into a commercial Upland cotton variety, a high-density simple sequence repeat(SSR) genetic linkage map was developed from a BC1F1 population of Gossypium hirsutum×Gossypium barbadense. The map comprised 2,292 loci and covered 5115.16 centi Morgan(c M) of the cotton AD genome, with an average marker interval of 2.23 c M. Of the marker order for 1,577 common loci on this new map, 90.36% agrees well with the marker order on the D genome sequence genetic map. Compared with five published high-density SSR genetic maps, 53.14% of marker loci were newly discovered in this map. Twenty-six quantitative trait loci(QTLs) for lint percentage(LP) were identified on nine chromosomes. Nine stable or common QTLs could be used for marker-assisted selection. Fifty percent of the QTLs were from G. barbadense and increased LP by 1.07%–2.41%. These results indicated that the map could be used for screening chromosome substitution segments from G. barbadense in the Upland cotton background, identifying QTLs or genes from G. barbadense, and further developing the gene pyramiding effect for improving fiber yield and quality.     

Detection of Quantitative Trait Loci for Yield and Drought Tolerance Traits in Soybean Using a Recombinant Inbred Line Population

To investigate the genetic basis of drought tolerance in soybean （Glycine max L. Merr.） a recombinant inbred population with 184 F2：7：11 lines developed from a cross between Kefengl （drought tolerant） and Nannong1138-2 （drought sensitive） were tested under water-stressed and well-watered conditions in field and greenhouse trials. Traits measured included leaf wilting coefficient, excised leaf water loss and relative water content as indicators of plant water status and seed yield. A total of 40 quantitative trait loci （QTLs） were identified： 17 for leaf water status traits under drought stress and 23 for seed yield under well-watered and drought-stressed conditions in both field and greenhouse trials. Two seed yield QTLs were detected under both well-watered and drought-stressed conditions in the field on molecular linkage group H and Dlb, while two seed yield QTLs on molecular linkage group C2 were found under greenhouse conditions. Several QTLs for traits associated with plant water status were identified in both field and greenhouse trials, including two leaf wilting coefficient QTLs on molecular linkage group A2 and one excised leaf water loss QTL on molecular linkage group H. Phenotypic correlations of traits suggested several QTLs had pleiotropic or location-linked associations. These results will help to elucidate the genetic basis of drought tolerance in soybean, and could be incorporated into a marker-assisted selection breeding program to develop high-yielding soybean cultivars with improved tolerance to drought stress.     

Construction of a Bacterial Artificial Chromosome Library of TM-1, a Standard Line for Genetics and Genomics in Upland Cotton

A bacterial artificial chromosome （BAC） library was constructed for Gossypium hirsutum acc. TM-1, a genetic and genomic standard line for Upland cotton. The library consists of 147 456 clones with an average insert size of 122.8 kb ranging from 97 to 240 kb. About 96.0% of the clones have inserts over 100 kb. Therefore, this library represents theoretically 7.4 haploid genome equivalents based on an AD genome size of 2 425 Mb. Clones were stored in 384 384- well plates and arrayed into multiplex pools for rapid and reliable library screening. BAC screening was carried out by four-round poiymerase chain reactions using 23 simple sequence repeats （SSR） markers, three sequence-related amplified polymorphism markers and one pair of primers for a gene associated with fiber development to test the quality of the library. Correspondingly, in total 92 positive BAC clones were identified with an average four positive clones per SSR marker, ranging from one to eight hits. Additionally, since these SSR markers have been localized to chromosome 12 （A12） and 26 （D12） according to the genetic map, these BAC clones are expected to serve as seeds for the physical mapping of these two homologous chromosomes, sequentially map-based cloning of quantitative trait loci or genes associated with important agronomic traits.     

Genetic analysis of morphological index and its related taxonomic traits for classification of indica/japonica rice

A doubled haploid population derived from anther culture of ZYQ8/JX17 F1, a typical indica and japonica hybrid, was used in this study. Morphological index and its related taxonomic traits were investigated in 121 DH lines. The quantitative trait loci (QTLs) for morphological index and its related taxonomic traits were analyzed. Two major QTLs for leaf hairiness, three QTLs for length/width of grain, one QTL for color of hull when heading, one QTL for hairiness of hull, two QTLs for length of the first and second panicle internode, and one major QTL and two QTLs for phenol reaction were detected. Four QTLs for morphological index were also identified on chromosomes 1, 3, 4 and 6, respectively, three of which on chromosomes 1, 3 and 6, respectively, were found to be located in the same chromosome regions where some QTLs for the related taxonomic traits were located.     

Analysis of QTLs for yield-related traits in Yuanjiang common wild rice (Oryza rufipogon Griff.)

Using an accession of common wild rice (Oryza rufipogon Griff.) collected from Yuanjiang County, Yunnan Province, China, as the donor and an elite cultivar 93-11, widely used in two-line indica hybrid rice production in China, as the recurrent parent, an advanced backcross populations were developed. Through genotyping of 187 SSR markers and investigation of six yield-related traits of two gen- erations (BC4F2 and BC4F4), a total of 26 QTLs were detected by employing single point analysis and inte...     

From the editor’s desk

Improving cotton fibre quality is a major breeding goal for Upland cotton in China. To investigate the genetic mechanisms of fibre quality, a diverse panel of 403 Upland cotton accessions was grown, and the fibre quality traits were measured in six different environments. Genotyping was performed with genomewide simple sequence repeats. A total of 201 markers were polymorphic and generated 394 allele loci, and 403 accessions were arranged into two subgroups using Structure software. Of the marker loci, 18.94% showed significant linkage disequilibrium (\(P< 0.05\)). A mixed linear model in association mapping showed that 51 associations were significant between 39 polymorphic loci and five fibre quality traits, according to best linear unbiased prediction, and in at least three of six environments. Of the 39 associated marker loci, 12 were coincident with previous studies. There were 41 typical accessions identified as containing favourable allele loci related to fibre quality traits. The identified favourable QTL alleles and typical accessions for fibre quality are excellent genetic resources for future cotton breeding in China.     

Detection of favorable alleles for yield and yield components by association mapping in upland cotton

Association mapping based on linkage disequilibrium provides a promising tool for dissecting the genetic basis underlying complex traits. To reveal the genetic variations of yield and yield components traits in upland cotton, 403 upland cotton accessions were collected and analyzed by 560 genome-wide simple sequence repeats (SSRs). A diverse panel consisting of 403 upland cotton accessions was grown in six different environments, and the yield and yield component traits were measured, and 560 SSR markers covering the whole genome were mapped. Association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model. Favorable alleles and typical accessions for yield traits were identified. A total of 201 markers were polymorphic, revealing 394 alleles. The average gene diversity and polymorphism information content were 0.556 and 0.483, respectively. Based on a population structure analysis, 403 accessions were divided into two subgroups. A mixed linear model analysis of the association mapping detected 43 marker loci according to the best linear unbiased prediction and in at least three of the six environments(??lgP?>?1.30, P?<?0.05). Among the 43 associated markers, five were associated with more than two traits simultaneously and nine were coincident with those identified previously. Based on phenotypic effects, favorable alleles and typical accessions that contained the elite allele loci related to yield traits were identified and are widely used in practical breeding. This study detected favorable quantitative trait loci’s alleles and typical accessions for yield traits, these are excellent genetic resources for future high-yield breeding by marker-assisted selection in upland cotton in China.     

A genome-wide association study of malting quality across eight U.S. barley breeding programs

Key message

We report malt quality QTLs relevant to breeding with greater precision than previous mapping studies. The distribution of favorable alleles suggests strategies for marker-assisted breeding and germplasm exchange.

Abstract

This study leverages the breeding data of 1,862 barley breeding lines evaluated in 97 field trials for genome-wide association study of malting quality traits in barley. The mapping panel consisted of six-row and two-row advanced breeding lines from eight breeding populations established at six public breeding programs across the United States. A total of 4,976 grain samples were subjected to micro-malting analysis and mapping of nine quality traits was conducted with 3,072 SNP markers distributed throughout the genome. Association mapping was performed for individual breeding populations and for combined six-row and two-row populations. Only 16 % of the QTL we report here had been detected in prior bi-parental mapping studies. Comparison of the analyses of the combined two-row and six-row panels identified only two QTL regions that were common to both. In total, 108 and 107 significant marker-trait associations were identified in all six-row and all two-row breeding programs, respectively. A total of 102 and 65 marker-trait associations were specific to individual six-row and two-row breeding programs, respectively indicating that most marker-trait associations were breeding population specific. Combining datasets from different breeding program resulted in both the loss of some QTL that were apparent in the analyses of individual programs and the discovery of new QTL not identified in individual programs. This suggests that simply increasing sample size by pooling samples with different breeding history does not necessarily increase the power to detect associations. The genetic architecture of malting quality and the distribution of favorable alleles suggest strategies for marker-assisted selection and germplasm exchange.

     

棉花资源收集、保存、评价与利用现状及未来

截至2010年12月,国家棉花种质中期库共保存棉花种质8868份,保存数量居世界第4位,其中陆地棉7362份、陆地棉野生种系350份、海岛棉633份、亚洲棉433份、草棉18份、野生种32份。共编目8503份,上交数据信息系统7527份,入长期库合格7298份,未能入长期库保存种质2194份。完善了繁殖更新技术,繁殖更新种质6550份,2001-2010年,共向704人次提供11507份棉花种质,年均1150份。2007-2010年对330份优异种质在河南安阳、江苏南京、新疆库车进行了精准鉴定,并进行了优异种质展示。近十年,创造了不同基因源且具有优质、专用、多抗、高产、高效等多个重要性状的优异基因聚合的新种质32份,并分别对12份棉花优异种质,从形态学、系谱和分子标记等方面进行了基因源和利用价值的分析,并定位相关基因。用简单重复序列(SSR)、EST-SSR、AFLP等分子标记,结合一种新方法"十进制数字串条形码",构建了优异种质特有的"分子身份证"。     

Genetic analysis of maize germplasm in the Korean Genebank and association with agronomic traits and simple sequence repeat markers

We assessed genetic and phenotypic variation in 105 maize germplasm accessions from RDA-Genebank of Korea and performed association analyses for 11 agronomical traits and 100 simple sequence repeats (SSR). Genetic diversity (GD) analysis revealed a total of 1104 alleles at the 100 SSR loci. The average number of alleles per locus was 11.0. The average GD and polymorphic information content values were 0.73 and 0.70, respectively. The average major allele frequency was 0.41. Population structure analysis indicated that these maize accessions comprised two major groups and one admixed group based on a membership probability threshold of 0.80. The two major groups contained 35 and 46 maize accessions. A mixed linear model of association analysis revealed five marker-trait associations with a significance level of P?≤?0.01 involving five SSR markers. A general linear model showed 72 marker-trait associations involving 42 SSR markers. We confirmed the presence in the general linear model associations of the five significant marker-trait associations (SMTAs) identified in the mixed linear model. For these SMTAs, two loci were associated with stem diameter and one locus each was associated with ear row number, leaf width, and leaf length. These results should prove useful for breeding new inbred lines by selecting parental lines using molecular markers and will help to preserve maize genetic resources in Korea.     

Evaluation and Exploration of Favorable QTL Alleles for Salt Stress Related Traits in Cotton Cultivars (G. hirsutum L.)

Soil salinization is one of the major problems in global agricultural production. Cotton is a pioneer crop with regard to salt stress tolerance, and can be used for saline-alkali land improvement. The large-scale detection of salt tolerance traits in cotton accessions, and the identification of elite quantitative trait loci (QTLs)/genes for salt-tolerance have been very important in salt tolerance breeding. Here, 43 advanced salt-tolerant and 31 highly salt-sensitive cultivars were detected by analyzing ten salt tolerance related traits in 304 upland cotton cultivars. Among them, 11 advanced salt-tolerance and eight highly salt-sensitive cultivars were consistent with previously reported results. Association analysis of ten salt-tolerance related traits and 145 SSRs was performed, and a total of 95 significant associations were detected; 17, 41, and 37 of which were associated with germinative index, seedling stage physiological index, and four seedling stage biochemical indexes, respectively. Of these associations, 20 SSR loci were simultaneously associated with two or more traits. Furthermore, we detected 117 elite alleles associated with salt-tolerance traits, 4 of which were reported previously. Among these loci, 44 (37.60%) were rare alleles with a frequency of less than 5%, 6 only existed in advanced salt-tolerant cultivars, and 2 only in highly salt-sensitive cultivars. As a result, 13 advanced salt-tolerant cultivars were selected to assemble the optimal cross combinations by computer simulation for the development of salt-tolerant accessions. This study lays solid foundations for further improvements in cotton salt-tolerance by referencing elite germplasms, alleles associated with salt-tolerance traits, and optimal crosses.     

Favorable QTL Alleles for Yield and Its Components Identified by Association Mapping in Chinese Upland Cotton Cultivars

Linkage disequilibrium based association mapping is a powerful tool for dissecting the genetic basis underlying complex traits. In this study, an association mapping panel consisting of 356 representative Upland cotton cultivars was constructed, evaluated in three environments and genotyped using 381 SSRs to detect molecular markers associated with lint yield and its components. The results showed that abundant phenotypic and moderate genetic diversities existed within this germplasm panel. The population could be divided into two subpopulations, and weak relatedness was detected between pair-wise accessions. LD decayed to the background (r ² = 0.1182, P≤0.01), r ² = 0.1 and r ² = 0.2 level within 12–13 cM, 17–18 cM and 3–4 cM, respectively, providing the potential for association mapping of agronomically important traits in Chinese Upland cotton. A total of 55 marker-trait associations were detected between 26 SSRs and seven lint yield traits, based on a mixed linear model (MLM) and Bonferroni correction (P≤0.05/145, −log₁₀ P≥3.46). Of which 41 could be detected in more than one environment and 17 markers were simultaneously associated with two or more traits. Many associations were consistent with QTLs identified by linkage mapping in previous reports. Phenotypic values of alleles of each loci in 41 stably detected associations were compared, and 23 favorable alleles were identified. Population frequency of each favorable allele in historically released cultivar groups was also evaluated. The QTLs detected in this study will be helpful in further understanding the genetic basis of lint yield and its components, and the favorable alleles may facilitate future high-yield breeding by genomic selection in Upland cotton.     

Molecular diversity, genomic constitution, and QTL mapping of fiber quality by mapped SSRs in introgression lines derived from Gossypium hirsutum?×?G. darwinii Watt

Because the genetic basis of current upland cotton cultivars is narrow, exploring new germplasm resources and discovering novel alleles relevant to important agronomic traits have become two of the most important themes in the field of cotton research. In this study, G. darwinii Watt, a wild cotton species, was crossed with four upland cotton cultivars with desirable traits. A total of 105 introgression lines (ILs) were successfully obtained. By using 310 mapped SSRs evenly distributed across the interspecific linkage map of G. hirsutum?×?G. barbadense, these 105 ILs and their corresponding parents were analyzed. A total of 278 polymorphic loci were detected among the 105 ILs, and the average length of introgression segments accumulated to 333.5?cM, accounting for 6.7?% of the whole genome. These lines included many variations. However, high similarity coefficients existed between lines, even between those derived from different parents. Finally, all the ILs and their upland cotton parents were used for association mapping of fiber quality in three environments. A total of 40 SSRs were found to be associated with five fiber quality indexes (P?相似文献   

Association mapping for yield and grain quality traits in rice (Oryza sativa L.)

Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm.     

陆地棉主要产量相关性状的SSR标记关联分析

高产优质育种是我国棉花育种的主要目标。寻找与目标性状关联的分子标记,可克服常规育种的盲目性,提高分子标记辅助选择育种的准确性。本研究对118份陆地棉种质资源的衣分、单铃重、单株铃数及子指等4个产量相关性状进行2年2点的表型鉴定,并利用覆盖全基因组的、有多态性的214对SSR标记进行标记与性状的关联分析。结果表明:118份材料的4个产量相关性状表型变异丰富,平均变异系数的变幅在6.1%~19.1%之间,且在各环境中表现较为稳定;基因型分析表明,214对标记共检测到460个等位变异,基因多样性指数平均为0.5151,PIC值平均为0.4587,表明该批标记具有较多的等位变异数和较高的基因多样性;群体结构分析表明该批材料可分为4个亚群,且各类群中材料与地理来源无对应关系;关联分析结果显示,在显著条件下(-log10P1.3,P0.05),共有39个标记位点能够在2个及2个以上的环境中同时检测到,其中有4个标记位点同时与2个以上性状相关联,进一步比较发现,有7个位点与前人研究结果一致,其余32个位点为新发现的位点。研究结果可为陆地棉产量性状遗传改良的分子标记辅助选择提供理论依据。