中国花生小核心种质与ICRISAT微核心种质的SSR遗传多样性比较

明确花生种质资源的遗传多样性和分布规律,对于发掘优良种质资源,选配优良亲本,拓宽育成品种的遗传基础具有重要意义。核心种质为种质资源的研究、评价和鉴定带来了方便。本研究从206对SSR引物中筛选26对引物对我国花生小核心种质和ICRISAT微核心种质共466份资源进行了遗传多样性分析,相似系数为0.49～0.99,鉴定出遗传差异最大的种质L2刚果(中国花生资源)与ICG12625(ICRISAT资源),相似系数为0.49。分析结果表明,多粒型花生的多态性信息量(0.761)和遗传多样性指数(0.97～1.11)均最大(平均相似系数最小,0.73～0.76),其次是普通型花生。中国花生种质资源与ICRISAT资源存在较大差异,尤其是ICRISAT的赤道型材料ICG12625,与中国花生资源的差异最大。相似系数和遗传多样性指数的分析结果均表明,我国花生种质资源的遗传多样性比ICRISAT资源丰富。     

Assessments of genetic diversity and anthracnose disease response among Zimbabwe sorghum germplasm

The USDA‐ARS National Plant Germplasm System maintains a Zimbabwe sorghum collection of 1235 accessions from different provinces. This germplasm has not been extensively employed in US breeding programmes due to the lack of phenotypic and genetic characterization. Therefore, 68 accessions from Zimbabwe were phenotyped, and evaluated for their anthracnose response for two consecutive years, and genetically characterized with 21 simple sequence repeat markers. Phenotypic analysis showed significant differences among accessions with plant height and panicle length being the most variable traits. Likewise, 25 accessions were anthracnose resistant, nine showed variable responses and 34 were susceptible. Genetic analysis identified 174 alleles with an average of 8.3 alleles and 11.8 genotypes per locus and a polymorphic information content of 0.60. These results reflect a moderate genetically diverse germplasm. Neighbour‐joining clustering analysis revealed that the majority of anthracnose‐resistant accessions showed high genetic relatedness; therefore, this germplasm might represent one to six new sources of resistances. Results presented herein show that the Zimbabwe collection contains valuable germplasm for breeding programmes and is an important source of anthracnose resistance.     

普通豇豆应用核心种质的SSR指纹图谱构建及多样性分析

不同种质资源群体的多样性及遗传背景分析可为种质资源收集保存及创新利用提供有效信息。对不同来源的88份普通豇豆应用核心种质资源进行了14个SSR位点的指纹图谱构建及多样性分析,共检测到39个等位变异,每对引物检测到2~5个,平均为2.79。多态信息含量（PIC）变幅为0.25~0.72,平均为0.58。UPGMA聚类结果显示,除了3对种质外,39个等位变异可将其他材料有效区分,且在遗传相似系数为0.63时,88份种质可分为4个类群,地理来源相同的材料有聚在一起的趋势。     

基于SSR分子标记的刺槐遗传多样性分析及核心种质的构建

刺槐(Robinia pseudoacacia)是一种极具发展利用潜能的林业生物质能源树种。为了解决刺槐林业生物质能源面临的原料短缺问题,本研究选取了中国北方7个地区的96个刺槐种质资源,运用筛选出的14对SSR引物进行标记,分析了其遗传多样性并构建核心种质。结果表明:刺槐种质资源的平均等位基因数(Na)为3.2143;平均有效等位基因数(Ne)为2.1840;平均Shannon’s信息指数(I)为0.8831;平均观测杂合度(Ho)为0.4055;平均预期杂合度(He)为0.5149,收集的刺槐种质存在丰富的遗传多样性。采用逐步聚类法进行核心种质构建,最终确定的核心种质共包含23份种质。通过t检测,核心种质遗传多样性与原始种质无显著差异,可以充分地代表原始种质资源。核心种质纤维素含量提高了2.17%,平均达到33.42%,适宜作为纤维素生物质能源原料。研究结果为刺槐种质资源的保护,管理和纤维素生物质能源化利用提供了丰富的理论依据和优良的种质材料。     

Mapping association of molecular markers and sheath blight (<Emphasis Type="Italic">Rhizoctonia solani</Emphasis>) disease resistance and identification of novel resistance sources and loci in rice

Sheath blight (ShB) disease caused by Rhizoctonia solani is one of the major threats to rice crop world-wide. Progress in breeding for resistant rice varieties is limited due to lack of highly resistant germplasm against sheath blight. In present study, diverse rice landrace were phenotyped against R. solani and resistant and moderately resistant sources were identified from the panel of 134 germplasm pool. Landrace Nizam shait showed resistance, where as Bidar local-2, Jigguvaratiga, NavaliSali, Jaddu and Tetep exhibited moderate resistance. Population structure was analysed by genotyping the accessions using 63 genome wide Rice Microsatellite markers which divided the mapping panel into two groups. Association mapping using GLM?+?Q model of TASSEL indicated significant association between twenty-one marker loci on nine chromosomes with ShB resistance with phenotypic variation (R²) ranging 3.02–22.71 per cent. We identified 13 new markers to be associated with ShB resistance. The present work validates previously identified eight markers flanking different shB QTLs. None of the allele from the tested markers was unique and common among resistant and moderately resistant landraces identified in this work except allele 420 bp of RM337 and allele 310 bp of RM5556 noticed only in Tetep. Our findings predict the possible presence of unreported QTL region in marker interval of RM337 and RM5556 on chromosome 8 for ShB resistance in Tetep which invites further investigation.     

Molecular diversity and population structure of the Ethiopian lentil (<Emphasis Type="Italic">Lens Culinaris</Emphasis> Medikus) genotype assessment using SSR markers

Knowledge of genetic diversity in germplasm is essential for formulating effective germplasm collection, conservation, utilization strategies in and crop improvement programs. It also provides an opportunity to take corrective steps infusing new genes to avoid risks associated with a narrow genetic bases. Genetic diversity analysis of 119 lentil genotypes of including 83 germplasm and 36 exotic genotypes from International Center for Agricultural Research in the Dry Areas was studied using 27 primers of simple sequence repeat (SSR) marker. Molecular analysis of variance showed variations of 82% within and 18% of the among population variance was explained. Degree of polymorphism observed among the populations was 100%. A total 122 alleles were detected, with 2 to 7 alleles per locus, with a mean of 4.52 alleles per locus. The estimated gene diversity value for 27 loci was 0.64. The average Shannon’s information index value of 1.19 was obtained showed the existence of high genetic variation within the genotypes. The genetic similarity indices ranged from 0.21 to 1.00. The SSR markers showed an average polymorphic information content (PIC) value of 0.58. Cluster analysis grouped the genotypes into five major clusters as distinct genetic populations. Diversity analyses revealed the existence of a high level of genetic variation among genotypes. This molecular diversity information provides a basis for future germplasm collection, utilization, and conservation strategies in gene banks and introducing exotic germplasm to widen the genetic base of the current lentil breeding population.     

大豆微核心种质在黄淮地区的区域适应性分析

运用主效可加互作可乘(AMMI)模型,对黄淮地区3省两年的60份大豆微核心种质数据进行了分析,目的是对参试种质的环境稳定性和适应性进行评价。结果表明,(1)株高、有效分枝数、百粒重和产量性状的基因型与环境互作效应(G×E)占总平方和的16.73%~24.57%,均达到极显著水平,说明有进一步进行稳定性分析的必要。(2)不同种质不同性状在各试验点具有不同的适应性,部分种质某一性状具有广泛适应性、而部分种质只在某一特定环境才能表现其潜力。本研究结果将为黄淮地区微核心种质在育种实践中的有效利用提供理论依据。     

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.     

大豆核心种质和微核心种质的构建、验证与研究进展

我国作物种质资源长期库中保存大豆资源2.3万余份,数量居世界之首。然而,在大豆新品种培育中的利用率仅为1%左右,导致大豆育成品种的遗传基础趋于狭窄。主要原因是缺少对其重要经济性状的鉴定,尤其是缺少多年多点的评价,难以有目的选择有重要价值的育种亲本。为了加速大豆种质资源的评价并促进其利用,在国家基础研究项目(973)的连续资助下,开展了“大豆核心种质构建(1998-2003)”和“大豆微核心种质基因多样性(2004-2009)”研究,目的是浓缩大豆资源的遗传多样性,强化其表型和基因型鉴定,为发掘和利用大豆资源中的优异基因提供指导。本文在研究构建不同比例(占总体2%~5%)大豆核心种质和大豆微核心种质(占总体1%)的同时,介绍了核心种质补充和完善的研究进展。为了验证核心种质的代表性,在构建方法方面,从SSR位点、样本组成、取样比例、低频率等位变异4个方面对代表性进行了分析,并用随机抽样方法对核心种质代表性进行了检测和验证。文中还介绍了利用核心种质和微核心种质在新基因发掘、种质创新和育种利用方面的研究进展,尤其介绍了与育种单位密切合作,建立基于核心种质的种质创新与利用体系的研究成效。围绕遗传多样性、核心种质利用方式进行了讨论,指出大豆核心种质为性状鉴定、新基因发掘、新种质创造和新品种培育等理论研究和实际应用提供材料基础,具有潜在的应用前景。实践证明,大豆种质资源的系统研究与利用,将促进我国大豆种质资源由数量保存型向研究应用型转变。     

Identification of natural variants affecting chlorophyll content dynamics during rice seedling development

Seedling vigour is an important characteristic in relation to crop growth and yield. Traits such as photosynthetic capacity and chlorophyll content contribute significantly to seedling establishment at the early growth stage in various crop species, including rice. A diverse panel of 227 rice varieties from several countries was evaluated to determine chlorophyll contents at multiple time points during the seedling stage using a soil–plant analysis development (SPAD) meter, a non‐destructive portable device. Using new statistical approaches, several chromosomal regions associated with variations in chlorophyll content in the third leaf at 13, 16 and 19 days after imbibition were detected. A single nucleotide polymorphism (SNP) cluster on the end of chromosome 11 was significantly associated with the onset of leaf senescence. This region was enriched with genes related to cell death and the stress response. We have identified rice germplasm showing delayed‐senescence phenotypes, these could be suitable donors and genetic resources for breeding, and the use of significant SNP markers associated with these traits could enhance the efficiency of their selection in breeding programmes.     

Population structure and linkage disequilibrium of ICRISAT foxtail millet (Setaria italica (L.) P. Beauv.) core collection

Use of diverse germplasm is a key factor which allows high level of resolution due to extensive recombination in the history. Therefore, population used in association mapping should posses as many phenotypes as possible. One of the methods to obtain most of the phenotypes is to construct the core collection. The ICRISAT foxtail millet core collection consisting of 155 accessions was genotyped using 72 simple sequence repeat (SSR) markers to investigate the genetic diversity, population structure and linkage disequilibrium (LD). A high degree of molecular diversity among the accessions was found, with an average of 16.69 alleles per locus. STRUCTURE analyses classify the accessions into four subpopulations (SP) based on SSR allelic diversity. The Neighbor joining clustering and the principal coordinate analysis were in accordance with the racial classification. The distribution of molecular genetic variation among and within the four SP and three races showed high degree of variability within each group, and low level of genetic distance (GD) among the groups. LD decay of <40 cM of GD in foxtail millet core collection was observed, which suggests that it could be possible to achieve resolution down to the 40 cM level. From this investigation, it is evident that the foxtail millet core collection developed at ICRISAT is very diverse and could be a valuable resource for trait association mapping, crop breeding and germplasm management.     

用SSR标记分析1949—2005年华南地区常规籼稻主栽品种遗传多样性及变化趋势

利用均匀分布于水稻基因组的300个SSR标记对95个华南地区不同年代常规籼稻主栽品种进行分析,研究该地区常规稻品种的遗传多样性及其变化趋势。检测到236个SSR标记有多态性,共获得776个等位基因,每个位点等位基因2~12个,平均3.29个,共有206个位点的等位基因数介于2~4个,占全部多态性位点的87.3%。多态性标记位点的PIC值平均为0.42,变化范围为0.041~0.790。不同染色体的位点多态性差异显著,其中第10染色体的位点平均等位基因数最多,PIC值最高,而第5染色体的位点平均等位基因数最少,PIC值最低;6个年代中,50~70年代育成品种包含等位基因数呈显著的上升趋势,70年代达最高值2.83,随后逐渐下降。分子方差分析(AMOVA)结果显示不同年代间遗传变异仅占总体变异的3.77%,但仍达极显著水平(P0.001)。不同年代育成品种的遗传距离(GD)呈下降趋势。聚类分析结果显示,在遗传相似系数(GS)为0.685处可将品种区分为5大类,表明华南地区各时期的常规稻品种遗传改良都是围绕少数骨干亲本进行的。试验结果显示,华南地区籼稻品种的遗传多样性狭窄且随年代而变化,70年代以后呈下降趋势,在今后的育种中应扩大亲本选材范围、拓宽育种亲本的遗传基础以提高育成品种的遗传多样性。     

基于SSR标记的80份烟草种质指纹图谱的构建及遗传多样性分析

利用均匀分布于烟草24个连锁群上的48个SSR标记对80份烟草材料进行分析。结果显示,48个SSR标记共扩增出211个等位基因,平均每个标记4.396个,Shannon′s信息指数I为1.034,多态信息含量值为0.229~0.905,观测杂合度（H_o）、期望杂合度（H_e）和Nei′s多样性指数（H）平均值分别为0.320、0.572、0.431。聚类结果表明,在遗传距离为0.68时可以将80份烟草种质分为2个类群。5个烟草居群间的遗传一致度在0.643~0.765范围内,遗传距离分布在0.268~0.442。筛选4对核心引物构建了不同烟草种质资源的数字指纹图谱, 可将这80份烟草种质资源全部区分开。本研究在分子水平上为筛选优质烟草种质资源、挖掘重要基因以及拓宽烟草育种遗传基础等工作提供科学依据。     

用于中国小豆种质资源遗传多样性分析SSR分子标记筛选及应用

以375份小豆核心种质为试验材料, 利用从小豆及其近缘种SSR引物中筛选出的13对引物进行遗传多样性分析。检测结果显示, 小豆种质资源具有丰富的遗传多样性, 共检测到133个等位变异, 每对SSR引物检测到等位变异4~19个, 平均10.23个, 国内各省多态信息含量(PIC)平均为0.561, 多态位点比例(P)平均为93.523%。聚类结果表明, 小豆资源遗传关系与生态分区间有明显的联系, 且东北地区资源与中南部资源遗传关系较近。湖北、安徽、陕西3省资源的PIC较高, 且基本位于主坐标三维图的中心区域, 推断湖北、安徽、陕西是中国栽培小豆的起源地或多样性中心。该结果有助于更好地对小豆种质资源进行收集、保护和利用。     

云南哈尼梯田红米地方品种遗传多样性分析

云南元阳哈尼梯田有丰富的水稻品种,特别是红米资源。本研究利用均匀分布于水稻基因组的100对简单序列重复（SSR）标记分析元阳哈尼梯田60份红米地方品种遗传多样性。100对SSR引物共扩增条带477个,平均每对引物扩增4.770个条带;有效等位基因数（Ne）从1.035~6.000,平均为2.518;香农多样性指数（I）为0.086~1.912,平均为1.016;多态性信息含量（PIC）范围为0.064~0.838,平均为0.519;基因杂合度（H）从0到0.950,平均为0.167;聚类分析可将60个红米品种分为两大类,第一类为籼稻亚种,包括57个水稻品种,第二类只有3个品种,为粳稻亚种。研究表明云南哈尼梯田水稻红米品种具有丰富的遗传多样性。     

基于SSR标记的雪茄烟种质资源指纹图谱库的构建及遗传多样性分析

为从分子水平研究我国雪茄烟种质资源的遗传多样性差异并建立雪茄烟品种的DNA指纹图谱数据库,本研究利用43对多态性好的SSR引物对220份雪茄烟种质进行遗传多样性分析,筛选出14对核心引物对雪茄烟种质进行指纹图谱的构建。结果表明,43对SSR引物在220份雪茄烟种质材料中共扩增出243个等位基因,平均每个标记5.65个,变幅为2~13,每个位点的多态性信息量(polymorphism information content,PIC)变化为0.2078~0.9087,平均为0.6360。有效等位基因数(number of effective alleles,N_e)范围为1.3081~11.7876,平均有效等位基因数为3.9077;观测杂合度(observed heterozygosity,H_o)变化范围为0.0828~0.7639,平均为0.3191;预期杂合度(expected heterozygosity,H_e)的变化范围为0.2361~0.9172,平均为0.6809;种群平均Shannon遗传多样性指数(Shannon genetic diversity index,I)为1.3756,遗传距离在0.0233~0.9286之间,平均遗传距离0.6816。聚类分析表明,在遗传距离为0.74处,可将供试雪茄烟资源分为3个类群。Structure群体遗传结构分析和主成分分析将所有的供试材料划分为2个类群。根据引物的分析和表型鉴定结果,确定良种、辅善和满耳朵,山东大叶和牡丹江05-1,Florida513和CA0701为异名同种,一个品种保留一份种质,剩余216份不同种质。从43对SSR引物中筛选出14对可区分所有供试材料的SSR引物作为核心引物构建了216个雪茄烟品种的指纹图谱。我国雪茄烟种质资源具有较高水平的遗传多样性,本研究构建的雪茄烟种质资源SSR指纹图谱库及遗传分析的结果在分子水平上为筛选、鉴定优质雪茄烟种质资源、挖掘重要基因以及拓宽雪茄烟遗传育种基础等工作提供科学依据。     

Development,characterization and mapping of microsatellite markers for lentil (Lens culinaris Medik.)

Lentil is the sixth most important pulse crop terms of production in the world, but the number of available and mapped SSR markers are limited. To develop SSR markers in lentil, four genomic libraries for (CA)n, (GA)n, (AAC)n and (ATG)n repeats were constructed. A total of 360 SSR primers were designed and validated using 15 Turkish lentil cultivars and genotypes. The most polymorphic repeat motifs were GA and CT, with a mean number of alleles per locus of 7.80 and 6.55, respectively. Seventy‐eight SSR primers amplified a total of 400 polymorphic alleles, whereas 71 SSR primers produced markers within the expected size range. For 78 polymorphic SSR primers, the average number of alleles per locus was 5.1 and PIC value ranged from 0.07 to 0.89, with an average of 0.58. A linkage map was constructed using 92 individual F₂ plants derived from a cross between Karacada? × Silvan, with 47 SSR markers. The SSR markers developed in this study could be used for germplasm classification and identification and mapping of QTL in lentil.     

Molecular characterization of endosperm and amino acids modifications among quality protein maize inbreds

Modifier loci in QPM play a vital role in achieving acceptable degree of kernel hardness and accumulation of lysine and tryptophan. This study was undertaken to characterize a set of diverse QPM inbreds using SSRs linked to endosperm and amino acids modifier loci for their effective utilization in the breeding programme. Significant variation was observed for endosperm modification (25–100% opaqueness), tryptophan (0.056–0.111%) and lysine (0.223–0.444%). Generally, inbreds with soft endosperm possessed more tryptophan and lysine than inbreds with higher vitreousness. SSRs generated 341 alleles with two to seven alleles per locus. The frequency of unique and rare alleles was more for amino acid modifications, compared to endosperm modifications. Phylogenetic analyses grouped the inbreds into three major clusters, and the study identified suitable crosses for accumulation of endosperm and amino acids modifiers. QPM inbreds with desirable modifications identified here would serve as suitable donor for both opaque2 and modifier loci in the marker‐assisted backcross breeding. Further, contrasting inbreds can be used for generating mapping populations to identify new modifier loci underlying both endosperm and amino acids modifications.     

湖南省饭豆地方种质资源遗传多样性的RAPD和ISSR分析

为揭示湖南省饭豆地方品种的遗传多样性,促进种质资源的有效保护和利用。本研究利用RAPD和ISSR标记分析了源于湖南省各地36份古老饭豆地方品种的遗传多样性,并采用UPGMA方法进行了遗传聚类分析。结果表明：12个RAPD引物和4个ISSR引物在供试材料中共扩增产生81条带型清晰的条带,平均每个引物扩增产生5.06个条带;其中59个为多态性条带,占总扩增条带的72.84%,具有多态性引物的PIC值在0.397~0.968之间;通过UPGMA法进行聚类分析表明供试材料的遗传相似系数在0.605~0.877之间,供试材料被分为4大类,且聚类结果表现明显的地域特征。本研究结果可为本省饭豆种质资源保护和育种研究提供理论依据。     

Rapid survey for presence of a blast resistance gene Pi-ta in rice cultivars using the dominant DNA markers derived from portions of the Pi-ta gene

The Pi‐ta gene in rice confers resistance to strains of the blast pathogen Magnaporthe grisea (Herbert) Borr. (anamorph Pyricularia oryza Cav.) containing the corresponding avirulence gene AVR‐Pita in a gene‐for‐gene fashion. The Pi‐ta gene is a typical nucleotide‐binding site type resistance gene. Nucleotide sequences distinguishing the resistant Pi‐ta and susceptible pi‐ta alleles were previously identified and used for developing DNA markers for a resistant Pi‐ta haplotype and three susceptible pi‐ta haplotypes. In the present study, the existence of the Pi‐ta gene in 141 rice germplasm accessions was rapidly determined using these markers, and the results were confirmed by inoculating rice germplasm with an M. grisea strain containing AVR‐Pita. The Pi‐ta gene was found in accessions from several major rice producing countries, including China, Colombia, Japan, Vietnam, the Philippines, Iran and the United States. The usefulness of DNA markers for rapid determination of the genotype of rice germplasm was thus demonstrated. The Pi‐ta gene also was found in rice cultivar known to contain the Pi‐ta² gene, although the allelic relationship of these genes remains to be determined. The presence of the Pi‐ta gene in landrace cultivars in several different geographical locations, the Philippines and Vietnam, other indica rice cultivars in China and Colombia suggest that the Pi‐ta gene may have spontaneously originated in indica rice cultivars. These results are useful for incorporating the Pi‐ta gene into advanced breeding lines by marker‐assisted selection for rice breeding programmes worldwide.