国家基因库野生大豆微核心样本遗传变异性的SSR标记分析

用70对SSR引物对96份野生大豆微核心种质样本进行了遗传多样性分析.结果检测出1278个等位变异,平均每个位点有18.3个.地理区域群体水平显示,遗传信息指数(PIC)和特异等位基因变异数(NUA)以东北地区最高,长江流域次之,华南地区最低.在地理区域个体水平,遗传多样性的特征值以华南地区最高,依次由南向北降低,东北最低.我国华南野生大豆和东北野生大豆有显著的遗传分化.聚类分析结果显示,国家基因库野生大豆保存样本中的典型野生大豆和半野生大豆之间存在明显的遗传差异;地理上,种质的地理遗传分组表现弱的地域性.本研究中半野生大豆杂合性明显高于典型野生型的结果,支持关于这个类型起源于栽培和野生大豆天然杂交的假说,栽培大豆的基因可能已经流入到野生种内,某些百粒重小于3g的种质可能也是来源于野生和栽培大豆的天然杂交后代分离.     

野生大豆地理群体的性状变异

中国是栽培大豆(Glycine max)的故乡,其原始种野生大豆(Glycine·soja)在我国大陆有大面积分布。种子富含蛋白质,是世人所瞩目的野生高蛋白基因资源。分布范围大约北纬24°—53°N,东经98°—135°E。其白花变种(G·soja var. albiflora)广见于东北和华北两大遗传多样性中心。狭叶白花变型(G·soja f. angustifolia)主要见于东北;华北和南方少见。狭叶变型(G·soja f. lanceolata)北方分布较多。野生大豆种子极小,一般百粒重在3克以下。在天然野生群体中通常还存在一类G·soja向G·max进化的中间过渡型半野生种(G·gracilis),种子较大,百粒重一般达到3—7克。电泳测定,天然野生群体中的酶或蛋白质标记基因证明,野生大豆是较严格的自花授粉植物,天然异交率     

不同进化类型大豆种子超氧物歧化酶的比较

本文对不同进化类型大豆种子超氧物歧化酶(SOD)进行了比较分析。结果表明:(1)供试三种进化类型大豆种子的 SOD 同工酶酶谱一致,均为7条,其中一条为 Ma-SOD,其余6条为 Cu-Zn-SOD。(2)SOD 活性表现为:野生类型明显高于中间类型,中间类型明显高于栽培类型。(3)随着大豆籽粒百粒重的增大,种胚的 SOD 活性降低。(4)种皮颜色由黑到黄,种皮的 SOD 活性降低。讨论了大豆种子 SOD 活性与 Sofa 亚属内大豆进化的关系。     

基于大豆胞囊线虫病抗性候选基因的SNP位点遗传变异分析

以我国363份栽培和野生大豆资源为材料, 对大豆胞囊线虫抗性候选基因(rhg1和Rhg4)的SNP位点(8个)进行遗传变异分析, 以期阐明野生和栽培大豆间遗传多样性及连锁不平衡水平差异。结果表明, 与野生大豆相比, 代表我国栽培大豆总体资源多样性的微核心种质及其补充材料的连锁不平衡水平较高(R²值为0.216)。在栽培大豆群体内, 基因内和基因间分别有100％和16.6％的SNP位点对连锁不平衡显著, 形成两个基因特异的连锁不平衡区间(Block)。在所有供试材料中共检测到单倍型46个, 野生大豆的单倍型数目(27)少于栽培大豆(31), 但单倍型多样性(0.916)稍高于栽培大豆(0.816)。单倍型大多数(67.4％)为群体所特有(31个), 其中15个为野生大豆特有单倍型。野生大豆的两个主要优势单倍型(Hap_10和Hap_11)在栽培大豆中的发生频率也明显下降, 推测野生大豆向栽培大豆进化过程中, 一方面形成了新的单倍型, 另一方面因为瓶颈效应部分单倍型的频率降低甚至消失。     

黑龙江省野生大豆、栽培大豆高异黄酮种质资源筛选

利用改进的高效液相色谱法(HPLC)检测了黑龙江省野生大豆(Glycine soja)、栽培大豆(G. max) 60份种质资源的异黄酮含量.结果表明,不同类型大豆种质资源异黄酮含量有明显遗传差异,变幅为416.2～6808.2μg/g,野生大豆高于栽培大豆,筛选出高异黄酮野生大豆种质资源4份、高异黄酮栽培大豆种质资源2份.     

大豆属不同进化类型植物导管分子的演化结构研究

使用光学显微镜技术,对大豆属不同进化类型植物次生木质部导管分子进行离析。实验结果表明：野生、半野生、半栽培和栽培大豆的导管分子相对长度、粗细差异较大,导管穿孔板形态亦不同。野生大豆导管分子保留了尾端,其它大豆导管分子尾端退化消失。大豆属植物导管的管间纹孔式多样,每种导管分子的形态代表了各自的演化地位,即：野生大豆原始→半野生大豆→半栽培大豆→栽培大豆导管分子的演化规律。     

大豆籽粒吸水遗传规律的探讨

对栽培大豆、野生大豆及其杂交后代籽粒进行吸水遗传规律的研究。结果表明：大豆籽粒吸水属于数量性状遗传,是由多基因控制的,吸水为显性,不易吸水为隐性,并且表现细胞质遗传效应和亲本效应。     

野生大豆耐盐性研究进展

野生大豆对于拓宽大豆种质遗传基础和丰富大豆种质基因库具有重要意义.该文从野生大豆的资源概况及优良性状、耐盐机理和利用野生大豆提高栽培大豆耐盐性等三个方面,对近年来国内外有关野生大豆耐盐性的解剖结构、生理基础、分子生物学基础等方面的研究进展进行了系统综述,并提出野生大豆通过茎叶表皮上的"腺体"及对Na+和Cl-的排斥性,实现对盐渍环境的颉颃作用.较强的抗氧化能力、大豆异黄酮代谢和耐盐基因也是其适应盐渍环境的重要原因.今后应对野生大豆耐盐机理的遗传学基础进行深入研究,并通过种群保护以保障野生大豆的发掘鉴定和创新利用.     

大明绿系选后代遗传多样性与高产特征分析

以内蒙古中东部地区61份绿豆品种大明绿系选后代为研究材料,通过对农艺性状的多样性及通径分析,明确了后代品系遗传类型及高产群体性状特征。结果表明,大明绿后代品系间性状差异显著,单株荚数变异系数最大为31.61%,其次为单株粒重28.05%,遗传多样性较丰富,多样性指数为单株荚数2.02,每荚粒数2.01,百粒重1.89,单株粒重1.96。后代品系主要有6种类型,各性状对单株粒重影响大小依次为:单株荚数>每荚粒数>百粒重>节数>株高。高产类型品系主要特征指标为单株粒重超过15 g,单株荚数超过30荚,每荚粒数8~10粒,株高48~60 cm,节数9~10节,百粒重可根据不同需求制定标准。     

大豆属植物茎的次生木质部结构研究

利用光学显微技术和扫描电镜技术,对大豆属Clycine L.的4种类型植物茎材进行比较解剖学研究.结果表明,4种类型植物的茎材横切面均为散孔材。野生大豆茎材多为单管孔.少见复管孔;半野生大豆具复管孔,少见多细胞的管孔链;半栽培大豆茎材中复管孔和管孔链较多;而栽培大豆的复管孔和管孔链更多且普遍.野生大豆单列射线多,多列射线少半野生大豆有少数多列射线;半栽培大豆多列射线较多;栽培大豆多列射线细胞组成的射线最多.大豆种植物的次生木质部导管的侵填体分布不同,各种结构的演化途径为野生大豆→半野生大豆→半栽培大豆→栽培大豆野生大豆结构较原始,栽培大豆最进化.     

Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation

The research objectives were to determine aspects of the population dynamics relevant to effective monitoring of gene flow in the soybean crop complex in Japan. Using 20 microsatellite primers, 616 individuals from 77 wild soybean (Glycine soja) populations were analysed. All samples were of small seed size (< 0.03 g), were directly collected in the field and came from all parts of Japan where wild soybeans grow, except Hokkaido. Japanese wild soybean showed significant reduction in observed heterozygosity, low outcrossing rate (mean 3.4%) and strong genetic differentiation among populations. However, the individual assignment test revealed evidence of rare long-distance seed dispersal (> 10 km) events among populations, and spatial autocorrelation analysis revealed that populations within a radius of 100 km showed a close genetic relationship to one another. When analysis of graphical ordination was applied to compare the microsatellite variation of wild soybean with that of 53 widely grown Japanese varieties of cultivated soybean (Glycine max), the primary factor of genetic differentiation was based on differences between wild and cultivated soybeans and the secondary factor was geographical differentiation of wild soybean populations. Admixture analysis revealed that 6.8% of individuals appear to show introgression from cultivated soybeans. These results indicated that population genetic structure of Japanese wild soybean is (i) strongly affected by the founder effect due to seed dispersal and inbreeding strategy, (ii) generally well differentiated from cultivated soybean, but (iii) introgression from cultivated soybean occurs. The implications of the results for the release of transgenic soybeans where wild soybeans grow are discussed.     

A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences

Background and Aims

It is essential to illuminate the evolutionary history of crop domestication in order to understand further the origin and development of modern cultivation and agronomy; however, despite being one of the most important crops, the domestication origin and bottleneck of soybean (Glycine max) are poorly understood. In the present study, microsatellites and nucleotide sequences were employed to elucidate the domestication genetics of soybean.

Methods

The genomes of 79 landrace soybeans (endemic cultivated soybeans) and 231 wild soybeans (G. soja) that represented the species-wide distribution of wild soybean in East Asia were scanned with 56 microsatellites to identify the genetic structure and domestication origin of soybean. To understand better the domestication bottleneck, four nucleotide sequences were selected to simulate the domestication bottleneck.

Key Results

Model-based analysis revealed that most of the landrace genotypes were assigned to the inferred wild soybean cluster of south China, South Korea and Japan. Phylogeny for wild and landrace soybeans showed that all landrace soybeans formed a single cluster supporting a monophyletic origin of all the cultivars. The populations of the nearest branches which were basal to the cultivar lineage were wild soybeans from south China. The coalescent simulation detected a bottleneck severity of K′ = 2 during soybean domestication, which could be explained by a foundation population of 6000 individuals if domestication duration lasted 3000 years.

Conclusions

As a result of integrating geographic distribution with microsatellite genotype assignment and phylogeny between landrace and wild soybeans, a single origin of soybean in south China is proposed. The coalescent simulation revealed a moderate genetic bottleneck with an effective wild soybean population used for domestication estimated to be ≈2 % of the total number of ancestral wild soybeans. Wild soybeans in Asia, especially in south China contain tremendous genetic resources for cultivar improvement.     

Fine-scale phylogenetic structure and major events in the history of the current wild soybean (Glycine soja) and taxonomic assignment of semi-wild type (Glycine gracilis Skvortz.) within the Chinese subgenus Soja

Wild and cultivated species of soybeans have coexisted for 5000 years in China. Despite this long history, there is very little information on the genetic relationship of Glycine soja and G. max. To gain insight into the major events in the history of the subgenus Soja, we examined 20 simple sequence repeat (SSR) markers of a large number of accessions (910). The results showed no significant differences between wild and semi-wild soybeans in genetic diversity but significant differences between G. soja and G. max. Ancestry and cluster analyses revealed that semi-wild soybeans should belong to the wild category and not to G. max. Our results also showed that differentiation had occurred not only among G. soja, G. gracilis, and G. max but also within G. soja and within G. gracilis. Glycine soja had 3 clear genetic categories: typical small-seeded (≤2.0 g 100-seed weight), dual-origin middle-seeded (2.0-2.5 g), and large-seeded plants (2.51-3.0 g). These last were genetically close to G. gracilis, their defining some traits having been acquired mainly by introgression from soybeans. Small-seeded G. gracilis (3.01-3.5 g) were genetically different from larger seeded ones (from 3.51 to 4.0 to over 10 g). Seed size predominated over seed coat color in evolutionary degree. Typical and large-seeded G. soja were found to have 0.7% and 12% introgressive cultivar genes, respectively. The genetic boundary of G. gracilis was at the range of 2.51-3.0 g of G. soja. In the great majority of wild accessions, traits such as white flowers, gray pubescences, no-seed bloom, and colored seed coats were likely introgressive from domesticated soybeans.     

The possible origin of thick stem in Chinese wild soybean (Glycine soja)

Thicker, erect stem and enlarged seeds are characteristic of the domestication of cultivated soybeans (Glycine max) from its progenitor, wild soybean (G. soja). Wild soybeans have different stem thicknesses but the thick stem as defined here appears in a small number of small-seeded wild soybeans (≤2.0 g/100-seeds) in China. However, little attention has been paid to this phenomenon in considering the origin of thick stem in wild soybean. Here, we addressed this question through the study of a mixed field of wild, semi-wild and cultivated soybeans. Thick-stemmed samples had lower sensitivity to light period, higher mean genetic diversity (H _e = 0.090, H = 0.535) and higher mean multilocus outcrossing rate (t _m = 9.77 %), while thin-stemmed plants were the opposite (H _e = 0.029, H = 0.416) and lower mean outcrossing rate (t _m = 5.88 %). F statistics calculations indicated that there was genetic differentiation between the thin and thick stems. UPGM cluster analysis showed that not only were thick-stemmed wild soybeans genetically different from thin-stemmed ones, but they were also genetically closer to semi-wild soybean, to varying degrees completely dependent on seed size. These data strongly implied that the plants with thick stems had more complicated genetic backgrounds than the thin-stemmed ones, and that they were related to cultivated soybeans. This study suggests that if plants have distinctly thick stems (an average 2.5-fold thicker than other thin-stemmed plants) or stems similar to semi-wild plants and/or near to local soybeans in a natural wild population adjacent to farmlands, such plants could be cultivar-introgressive offspring.     

Population Structure and Domestication Revealed by High-Depth Resequencing of Korean Cultivated and Wild Soybean Genomes

Despite the importance of soybean as a major crop, genome-wide variation and evolution of cultivated soybeans are largely unknown. Here, we catalogued genome variation in an annual soybean population by high-depth resequencing of 10 cultivated and 6 wild accessions and obtained 3.87 million high-quality single-nucleotide polymorphisms (SNPs) after excluding the sites with missing data in any accession. Nuclear genome phylogeny supported a single origin for the cultivated soybeans. We identified 10-fold longer linkage disequilibrium (LD) in the wild soybean relative to wild maize and rice. Despite the small population size, the long LD and large SNP data allowed us to identify 206 candidate domestication regions with significantly lower diversity in the cultivated, but not in the wild, soybeans. Some of the genes in these candidate regions were associated with soybean homologues of canonical domestication genes. However, several examples, which are likely specific to soybean or eudicot crop plants, were also observed. Consequently, the variation data identified in this study should be valuable for breeding and for identifying agronomically important genes in soybeans. However, the long LD of wild soybeans may hinder pinpointing causal gene(s) in the candidate regions.     

Genetic diversity and population structure of Korean wild soybean (Glycine soja Sieb. and Zucc.) inferred from microsatellite markers

Korea is considered one of the centers of genetic diversity for cultivated as well as wild soybeans. Natural habitats of wild soybeans are distributed across the Korean mainland and the islands surrounding the Korean peninsula. In this study, the genetic diversity of 100 mainland Korean wild soybean accessions was evaluated by using 42 simple sequence repeat markers covering 17 soybean chromosomes. All analyzed loci were polymorphic and a total of 114 alleles were found. The observed average genetic diversity was low (0.4). The results showed that the 100 selected accessions did not exactly follow the geographical distribution. These results were further confirmed by the phylogeny inferred from five morphological characteristics (i.e., leaf shape, leaf area, plant shape, seed area, and 100-seed weight). Together, the genetic and morphological evaluations suggested conclusively that the selected population did not follow the geographical distribution pattern. The present study could provide useful information for the ex situ conservation and exploitation of wild soybean accessions in soybean improvement stratagems, and will aid in further understanding about the phylogeography of the species in the Korean center of diversity.     

The genetic diversity of annual wild soybeans grown in China

Annual wild soybeans (Glycine soja), the ancestors of cultivated soybeans (G. max), are important sources of major genes for resistance to pests, diseases and environmental stresses. The study of their genetic diversity is invaluable for efficient utilization, conservation and management of germplasm collections. In this paper, the number of accessions, the variation of traits, the genetic diversity indexes (Shannon index) and the coefficient of variation were employed to study the geographical distribution of accessions, genetic diversity of characters and genetic diversity centers of annual wild soybean by statistical analysis of the database from the National Germplasm Evaluation Program of China. Most annual wild soybeans are distributed in Northeast China, and the number of accessions decreases from the Northeast to other directions in China. The genetic diversity indexes (Shannon index) were 0.49, 0.74, 0.02, 0.55, 1.45, 2.41, 1.27 and 1.89 for flower color, sootiness of seed coat, cotyledon color, pubescence color, hilum color, leaf shape, stem type and seed color, respectively. Coefficients of variation were 7.1%, 28.7%, 76.43% and 18.2% for protein content, oil content, 100-seed weight and days to maturity, respectively. Three genetic diversity centers, the Northeast, the Yellow River Valley and the Southeast Coasts of China, are proposed based on the geographical distribution of the number of accessions, genetic diversity and the multivariate variation coefficient. Based on these results and Vavilov’s theory of crop origination, two opposing possible models for the formation of the three centers are proposed, either these centers are independent of each other and the annual wild soybeans in these centers originated separately, or the Northeast center was the primary center for annual wild soybeans in China, while the Yellow River Valley center was derived from this primary center and served as the origin for the Southeast Coast center. Received: 25 June 2000 / Accepted: 18 October 2000     

The origin and fate of morphological intermediates between wild and cultivated soybeans in their natural habitats in Japan

The spread of transgenes into the genome of wild soybean is a concern when transgenic and wild soybeans are planted sympatrically. The objectives of this study were to investigate the origin and fate of morphological intermediates between wild and cultivated soybeans in their natural habitats in Japan. Twenty nuclear microsatellite and two chloroplast dCAPS markers were used to evaluate genetic variation of 468 wild, 17 intermediate, and 12 cultivated soybean samples collected from six sites between 2003 and 2006. Allelic differentiation of microsatellite markers between wild and cultivated soybeans was sufficient to detect their hybrids. Based on levels of observed heterozygosity, intermediate soybean plants were from two generations: either F₁ or an early segregating generation. Genetic admixture analysis and parentage assignment analysis revealed that the parents of all intermediate soybean plants could be assigned to a particular wild soybean plant and late‐maturing cultivar. The chloroplast DNA haplotypes revealed that all intermediate soybean plants originated from gene flow from cultivated to wild soybeans at all sites. Based on monitoring at both the phenotypic and molecular levels, hybrids quickly disappeared from natural habitats, and secondary gene flow from these plants to wild soybean was not detected. Thus, while gene flow from transgenic soybean into wild soybean can occur, gene introgression appears to be rare in natural habitats in Japan. This is the first report on the detection of gene flow from cultivated to wild soybean at the molecular level.     

Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression

Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3) high heterozygous rates (0.19–0.49) were observed in several semi-wild lines; and (4) over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.