Association mapping of yield-related traits and SSR markers in wild soybean (Glycine soja Sieb. and Zucc.)

Wild soybean, the progenitor of cultivated soybean, is an important gene pool for ongoing soybean breeding efforts. To identify yield-enhancing quantitative trait locus (QTL) or gene from wild soybean, 113 wild soybeans accessions were phenotyped for five yield-related traits and genotyped with 85 simple sequence repeat (SSR) markers to conduct association mapping. A total of 892 alleles were detected for the 85 SSR markers, with an average 10.49 alleles; the corresponding PIC values ranged from 0.07 to 0.92, with an average 0.73. The genetic diversity of each SSR marker ranged from 0.07 to 0.93, with an average 0.75. A total of 18 SSR markers were identified for the five traits. Two SSR markers, sct_010 and satt316, which are associated with the yield per plant were stably expressed over two years at two experimental locations. Our results suggested that association mapping can be an effective approach for identifying QTL from wild soybean.     

糯玉米自交系SSR标记遗传多样性及群体遗传结构分析

为了解糯玉米种质的遗传基础,利用29对SSR标记对87份糯玉米自交系进行遗传多样性分析,共检测出180个等位变异,平均每个位点6个等位变异,多态性信息含量变幅为0.308～0.915,平均为0.572。材料间遗传相似系数为0.49～0.93,平均为0.66。通过聚类分析UPGMA (unweighted pair-group method with arithmetic means)方法在遗传相似系数0.64处将87份糯玉米自交系划分为4个类群,分别包含9、66、10和2份材料。此外,利用Structure群体遗传结构分析也将87份糯玉米自交系分为4个类群,分别包含24、25、19和19份材料;进一步分析表明,供试群体中大部分糯玉米自交系的遗传变异较单一。本研究为糯玉米新品种选育和遗传进化分析提供了种质基础和理论依据。     

Genetic analysis for the leaf pubescence density and water status traits in soybean [Glycine max (L.) Merr.]

Leaf pubescence density (PD) is an important component for the adaptation of soybean [ Glycine max (L.) Merr.] to drought-prone environment. Quantitative trait loci (QTL) controlling PD on the upper surface of leaf blade (PDU), PD on the lower surface of leaf blade (PDL), leaf wilting coefficient (WC) and rate of excised leaf drying (ELD) were identified using recombinant inbred lines (RILs) population from the cross between soybean cultivars 'kefeng1' and 'nannong1138-2' at the field soil drought stress stage from the mid-end of stem elongation to onset of flowering. A total of 20 QTLs were detected on molecular linkage groups (MLGs) A2, D1b, E, H, G and I with individual QTL explained 4.49–23.56% of phenotypic variation by composite interval mapping. The QTLs for PD on MLG H were mapped to near Ps locus while the QTLs on MLG D1b were located near Rsc-7 . Three genome regions for PD and water status traits on MLGs A2, D1b and H were associated. This study revealed that leaf surface PD may play an important role in the soybean drought tolerance.     

Mapping quantitative trait loci for yield-related traits in soybean (Glycine max L.)

Development of soybean cultivars with high seed yield is a major focus in soybean breeding programs. This study was conducted to identify genetic loci associated with seed yield-related traits in soybean and also to clarify consistency of the detected QTLs with QTLs found by previous researchers. A population of 135 F_2:3 lines was developed from a cross between a vegetable soybean line (MJ0004-6) and a landrace cultivar from Myanmar ({"type":"entrez-nucleotide","attrs":{"text":"R18500","term_id":"772110","term_text":"R18500"}}R18500). They were evaluated in the experimental field of Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand in a randomized complete block design with two replications each in 2011 and 2012 growing seasons. The two parents exhibited contrasting characteristics for most of the traits that were mapped. Analysis of variance showed that the main effects of genotype and environment (year) were significant for all studied traits. Genotype by environment interaction was also highly significant for all the traits. The population was genotyped by 149 polymorphic SSR markers and the genetic map consisted of 129 SSR loci which converged into 38 linkage groups covering 1156 cM of soybean genome. There were 10 QTLs significantly associated with seed yield-related traits across two seasons with single QTLs explaining between 5.0% to 21.9% of the phenotypic variation. Three of these QTLs were detected in both years for days to flowering, days to maturity and 100 seed weight. Most of the detected QTLs in our research were consistent with earlier QTLs reported by previous researchers. However, four novel QTLs including SF1, SF2 and SF3 on linkage groups L and N for seed filling period and PN1 on linkage group D1b for pod number were identified in the present study.     

Genetic diversity of garlic (Allium sativum L.) germplasm from China by fluorescent‐based AFLP,SSR and InDel markers

Garlic (Allium sativum L.), an asexually propagated crop, is an important vegetable and medicinal plant. China is the biggest garlic producer in the world; however, the genetic background of garlic from China is not well understood. In this study, population structure and clustering analysis of garlic germplasm was performed using amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR) and insertion–deletion (InDel) markers. Among 212 accessions of garlic, genetic diversity analysis identified 546 alleles amplified by AFLP, SSR and InDel primers, and 492 of these were polymorphic. All accessions were divided into five groups by structure analysis and neighbor‐joining clustering. Most traits, including allicin content, were only slightly affected by population structure, which indicated that this germplasm can be used as populations for association mapping. The results provide a molecular basis for understanding the genetic diversity of the garlic germplasm preserved in China.     

基于SNP和InDel标记的巴西木薯遗传多样性与群体遗传结构分析

为了对巴西木薯种质资源进行遗传多样性、亲缘关系和群体遗传结构分析,本研究利用了7946个SNPs和1997个InDels分子标记,通过ADMIXTURE软件进行群体结构分析、GCTA软件进行主成分分析。结果显示,巴西木薯被划分为9个亚群。这与利用PHYLIP进行的聚类分析结果大概一致,其中亚群1、亚群2、亚群4、亚群6和亚群8能较好地分别聚在一起,而其他亚群中的样品大致能聚在一起,且样品间有一定的交叉。巴西木薯种质资源遗传多样性指数(0.274)高于中国、尼日利亚等,其中巴西木薯亚群5具有相对较高的遗传多样性水平(0.29)。巴西木薯各亚群的群体遗传分化程度较低(群体分化指数在0.03~0.15之间),但高于中国木薯种质资源的群体分化指数。各木薯材料间的遗传距离变幅为0.084~0.297,平均遗传距离为0.228。本研究结果可为后续关联分析发掘优良等位基因及引种提供依据。     

基于SNP和InDel标记的巴西木薯遗传多样性与群体遗传结构分析

As a typical tropical crop, cassava (Manihot esculenta Crantz) has the characteristics of drought resistance, barren resistance, high biomass and so on. In addition to being used for food and forage, it can also be used for production, processing and starch extraction. Due to highly heterozygous cassava genome, breeding is more difficult. Enriching the genetic diversity of cassava germplasm, comprehensively evaluating its genetic background and traits, and discovering superior alleles that control excellent traits are of great significance for cassava breeding in the future. In order to analyze the genetic diversity, genetic relationship and population structure of cassava germplasm in Brazil, 7946 SNPs and 1997 InDels molecular markers were used. Population structure analysis was performed by ADMIXTURE software, and principal component analysis was performed by GCTA software. Brazilian cassava was divided into nine subgroups, and was roughly consistent with the results of cluster analysis using PHYLIP. Among them, subgroup 1, subgroup 2, subgroup 4, subgroup 6, and subgroup 8 could be clustered together respectively, while the samples of other subgroups could be roughly clustered, and there was a certain cross between the samples. The genetic diversity of cassava germplasm in Brazil (0.274) was higher than the genetic diversity level of cassava germplasm in China and Nigeria. Subgroup 5 of Brazil cassava had a relatively high genetic diversity (0.29). The genetic differentiation of subgroups was low (the genetic differentiation vary from 0.03 to 0.15), but higher than domestic cassava germplasm. The genetic distance between cassava accessions varied from 0.084 to 0.297, with the average of 0.228. The results of this study can provide a basis for subsequent association analysis to identify great alleles and introduction.     

Genetic variation in soybean (Glycine max (L.) Merril) for cookability and water absorption during cooking

Summary Improvement of cookability is an important objective in breeding of food legumes. The present study was undertaken to investigate variation in cookability in soybean. Genetic variation was observed among lines from two crosses. Absence of associations between cookability and protein content, oil content and grain yield indicate that selection for cookability can be achieved without adversely affecting the expression of these characters.     

Genetic differentiation between summer and autumn maturing cultivars of soybean (Glycine max (L.) Merrill) in Kyushy district of Japan

Summary 135 soybean landraces and pure line selections from Kyushu district fo Japan were assayed for isozyme and seed protein loci in order to determine the genetic structure groups of summer and autumn maturing cultivars. Out of the 16 tested loci, Dial, Enp, Estl, and Ti exhibited a marked difference in allelic frequency between both groups. The summer cultuvar groups had a high frequency for Dial-b, Enp-b, Estl-a and Ti-b, whereas Dial-a, Enp-a, Estl-b, and Ti-a were predominant in the autumn groups. The analysis of multi-locus genotypes revealed that both groups mostly consisted of different multi-locus genotypes. The allelic combination Dial-b Enp-b Estl-a Ti-b was most frequently observed in the summer cultivars, whereas four genootypes, Dial-a Enp-a Estl-a Ti-a, Dial-a Enp-a Estl-b Ti-a, Dial-a Enp-b Estl-b and Dial-a Enp-a Estl-b Ti-b, occupied most of the autumn cultivars. These results indicated that both groups were appreciably differentiated from each other. The summer cultivar groups also included a few accessions having the multi-locus genotypes observed predominantly in the autumn groups or Acol-b charcteristic of the landraces native to northern Japan. It seems likely that the summer cultivar groups was not phyletically derived from a single common ancestor, but partly involves the landraces with early maturity derived from northern Japan. Dial, Enp, Estl and Ti are useful genetic markers ot trace the origin and dissemination paths of Japanse soybean landraces.     

Genetic variability of drought-avoidance root traits in the mini-core germplasm collection of chickpea (Cicer arietinum L.).

Extensive and deep root systems have been recognized as one of the most important traits for improving chickpea (Cicer arietinum L.) productivity under progressively receding soil moisture conditions. However, available information on the range of variation for root traits is still limited. Genetic variability for the root traits was investigated using a cylinder culture system during two consecutive growth seasons in the mini-core germplasm collection of ICRISAT plus several wild relatives of chickpea. The largest genetic variability was observed at 35 days after sowing for root length density (RLD) (heritability, h ² = 0.51 and 0.54) across seasons, and followed by the ratio of plant dry weight to root length density with h ² of 0.37 and 0.50 for first and second season, respectively. The root growth of chickpea wild relatives was relatively poor compared to C. arietinum, except in case of C. reticulatum. An outstanding genotype, ICC 8261, which had the largest RLD and one of the deepest root system, was identified in chickpea mini-core germplasm collection. The accession ICC 4958 which was previously characterized as a source for drought avoidance in chickpea was confirmed as one with the most prolific and deep root system, although many superior accessions were also identified. The chickpea landraces collected from the Mediterranean and the west Asian region showed a significantly larger RLD than those from the south Asian region. In addition, the landraces originating from central Asia (former Soviet Union), characterized by arid agro-climatic conditions, also showed relatively larger RLD. As these regions are under-represented in the chickpea collection, they might be interesting areas for further germplasm exploration to identify new landraces with large RLD. The information on the genetic variability of chickpea root traits provides valuable baseline knowledge for further progress on the selection and breeding for drought avoidance root traits in chickpea.     

Genetic diversity,population structure,pollen morphology and cross‐compatibility among Chinese Cymbidiums

A total of 85 Chinese Cymbidiums and one Zygopetalum were collected and analysed using 29 simple sequence repeats (SSRs) and 12 intersimple sequence repeats (ISSRs). These Chinese Cymbidiums are some of the most popular cultivars in market. The pairwise genetic distance between these accessions averaged 0.897, ranging from 0.259 to 1.000. A model‐based clustering analysis revealed five genetic groups with serious admixture ancestry, as indicated by a fixation index of 0.156 and only 10.67% genetic variation among groups. By analysing the cross‐compatibility and pollen morphology, Chinese Cymbidiums are revealed to have high compatibility for intra‐ and interspecific crosses. Notably, Zygopetalum mackayi had high compatibility with Chinese Cymbidiums and shared similar morphologies in terms of pollinia and pollen grain. This study is the first to report a successful cross between Zygopetalum and Chinese Cymbidiums. The high compatibility offers the potential for introducing Zygopetalum mackayi's superior traits into Chinese Cymbidiums. The similar pollen morphology as well as the low genetic differentiation might be related to the high cross‐compatibility among these accessions.     

Genetic diversity and population structure of the selected core set in Amaranthus using SSR markers

The genus Amaranthus has gained much attention, particularly for its high economic and nutritional value. It is a genus of taxonomic complexity with many interspecific hybrids. For effective conservation and management of the germplasm collected, the development of a core set of accessions is especially important. A core set of 63 accessions was successfully developed from an entire collection of 634 accessions using the powercore 1.0. Among the tested methods for developing the core set – the advanced M strategy using the modified heuristic method (HCC), randomly chosen collections and stratified random collections – HCC was found to be best, with 100% coverage of alleles and minimum redundancy. Allele frequency distribution of the core set developed with HCC was highly correlated with that of entire collections (r = 0.91). Model‐based structure analysis revealed the presence of three subpopulations and 11 admixtures in the selected core set, which is basically consistent with clustering based on the genetic distance. The results from this study will provide effective information for future germplasm conservation and improvement programmes in Amaranthus.     

Quantitative trait locus analysis for soybean (Glycine max) seed protein and oil concentrations using selected breeding populations

Soybean seed protein and oil concentrations are important traits that directly affect the quality of soyfoods. Many studies and breeding programmes have been conducted to find major quantitative trait loci (QTL) that regulate protein and oil concentrations and to develop soybean cultivars with high protein and/or oil content. The purpose of this study was to identify these QTL using a selected breeding population. The population was tested in field conditions over a period of 3 years. Seed protein and oil concentrations were measured each year. Single‐nucleotide polymorphisms (SNPs) were used to construct genetic map using a 180K SoyaSNP array, which identified 1,570 SNPs. We identified 12 QTL for seed protein, 11 for seed oil concentration and four for both traits. Among these, 17 QTL were closely mapped to previously reported QTL, whereas ten sites were novel. Several QTL were detected across at least two experimental years. These loci are good candidate QTL for optimal seed protein and oil concentrations. Our results demonstrate that favourable target QTL can be successfully identified using selected breeding populations.     

Assessing genetic diversity in the cassava (Manihot esculenta Crantz) germplasm collection in Brazil using PCR-based markers

Knowledge of the origin, organization and nature of the cassava (Manihot esculenta Crantz) germplasm collection in Brazil is incomplete due to lack of critical information on several aspects of the collection. This study verifies the utility of SSR-primed PCR markers for germplasm assessment and then utilizes these markers as well as RAPD's to characterize the Brazilian collection. We specifically address the following questions: 1)what is the relationship of morphologically closely related species to cultivated cassava? 2) What is the genetic diversity of cultivars within and between different habitats in Brazil? 3) Do agronomic traits and molecular markers reveal the same relationship among cassava accessions? 4) How complete is the Brazilian cassava collection and how well is it represented in the Word Core Collection of cassava, maintained by CIAT? Results of the interspecific studies of cassava and its wild relatives confirms the close relationship of cassava, Manihot esculenta ssp. esculenta to Manihot esculenta ssp. flabellifolia as well identifying several other closely related wild species. Next, PCR-based markers indicate a strong grouping of varieties related to the region of cultivation in Brazil. Moreover, important regions such as Cerrados and Amazon are relatively poorly represented in germplasm collections. Interestingly, the relationships of accessions based on agronomic traits are not fully congruent with relationships revealed with RAPD markers. Finally, the genetic diversity of the Brazilian cassava collection is not fully represented in the Core of the Word Core Collection of CIAT.     

大豆叶片表面结构与蒸腾的关系

用光镜和扫描电镜对大豆叶片进行观察的结果表明,气孔和表皮毛密度及表皮毛分布方式在上下表皮间存在差异。中层叶片气孔密度高于上层和下层叶片;而中层叶片表皮毛密度则低于上层和下层叶片。不同品种叶片表面结构状态有所不同。蒸腾速率测定结果表明,大豆多数品种蒸腾日变化呈单峰曲线,中层叶片的蒸腾速率大于上层和下层叶片     

Genetic variation in South Korean natural populations of wild soybean (Glycine soja)

Summary Wild relatives are valuable genetic resources for crop improvement. Evaluating genetic variation in these species is not only important for their use in breeding programs, but will also provide information about evolution of crops. Seeds representing six natural populations were used to study the level of variation in the South Korean wild soybean. Electrophoretic assays of the seeds on horizontal slab gels were conducted to determine the genotypes of each natural plant at 35 loci in 17 isozymes and one protein. The results indicated a surprisingly high variation. The number of alleles at each locus was as high as four. Seventy two of the 94 reported alleles for the 35 loci were present in these populations. The average number of alleles per locus, 99% polymorphism and the expected heterozygosity in the total population were 2.1, 77.1% and 0.215, respectively. This amount of variation was not only higher than that reported for 857 soybean cultivars and wild soybean populations from other geographic regions, but also higher than the average for 123 self-fertilized plant species and 473 plant species of all mating systems. The high variation in the South Korean wild soybean as well as cultivated soybean indicated in this and other population genetic studies prompts us to propose that South Korea is one of the major soybean gene centers.