Evaluation of soybean germplasm conserved in NIAS genebank and development of mini core collections

Genetic variation and population structure among 1603 soybean accessions, consisted of 832 Japanese landraces, 109 old and 57 recent Japanese varieties, 341 landrace from 16 Asian countries and 264 wild soybean accessions, were characterized using 191 SNP markers. Although gene diversity of Japanese soybean germplasm was slight lower than that of exotic soybean germplasm, population differentiation and clustering analyses indicated clear genetic differentiation among Japanese cultivated soybeans, exotic cultivated soybeans and wild soybeans. Nine hundred ninety eight Japanese accessions were separated to a certain extent into groups corresponding to their agro-morphologic characteristics such as photosensitivity and seed characteristics rather than their geographical origin. Based on the assessment of the SNP markers and several agro-morphologic traits, accessions that retain gene diversity of the whole collection were selected to develop several soybean sets of different sizes using an heuristic approach; a minimum of 12 accessions can represent the observed gene diversity; a mini-core collection of 96 accession can represent a major proportion of both geographic origin and agro-morphologic trait variation. These selected sets of germplasm will provide an effective platform for enhancing soybean diversity studies and assist in finding novel traits for crop improvement.     

黑龙江省大豆遗传结构及遗传多样性分析

利用22个表型性状和60个微卫星(simple sequence repeat, SSR)位点对黑龙江省140份代表性种质(78份地方品种和62份育成品种)进行分析, 根据UPGMA (unweighted pair group method with arithmetic mean)和Model-base对SSR数据进行遗传结构划分。结果表明, 参试品种可分为2大类群, 第II类群的各项多样性指标均高于第I类群, 2个类群遗传距离为0.2427;PCO结果显示这2个类群分布在不同区域, 这与地理来源和育成年代密切有关。依据品种类型分为育成品种和地方品种两组, 后者的各项多样性指标均高于前者, 两组间的遗传距离为0.1131。依据表型数据的PCO分析表明, 分布区域与品种类型有关, 与SSR结构分类的结果吻合度低, 两组品种主要在3个主成分的6个表型性状上有所不同。它们不是2个相对独立的遗传群体, 根据分子标记和表型分类各有特点;建议在种质遗传多样性研究中将分子数据和表型数据结合起来。     

Genetic diversity of wild and cultivated soybeans growing in China revealed by RAPD analysis

To evaluate the genetic diversity and to clarify the genetic relationships of wild and cultivated soybeans growing in China, 21 wild soybean accessions and 27 cultivated soybean landraces were analysed by using the random amplified polymorphic DNA method. The data show that wild soybean has a higher genetic variation than cultivated soybean, indicating that genetic variation has been reduced by domestication of wild soybean. Based on Nei's genetic similarity coefficient, all the accessions were classified into two major clusters, corresponding to wild and cultivated varieties of soybean. Furthermore, within each species, the accessions tend to form sub‐clusters that are in agreement with their geographical origins, demonstrating that an extensive geographical genetic differentiation exists in both species. For cultivated soybean, the varieties from the same geographical region but with different seasonal types were found to have closer genetic relationships than varieties from different geographical regions but with the same seasonal type. This result indicates that geographical differentiation plays a key role in the genetic differentiation of both wild and cultivated soybeans. Cultivated soybean varieties with different seasonal types in a region might have been established mainly from the local genotypes.     

大豆Soja亚属内种子大小的遗传差异及半野生类型分类归属

Soja亚属包括野生、半野生和栽培大豆三种类型,其中半野生型变异丰富,与野生和栽培大豆形态重叠。然而半野生大豆是属于野生种内还是栽培种的变异类型还存在争议。本研究使用421份包括两组野生大豆百粒重类型、三组半野生大豆百粒重类型和小粒秣食豆类型大豆地方品种对Soja亚属内进行了SSR标记的遗传多样性差异评价和对半野生大豆的分类地位归属问题进行了分析。结果显示,小粒组野生大豆(2.5g以下)和大粒组(2.5~3.0g)有明显的分化。大粒野生大豆和小粒半野生大豆(3.01~5.0g)遗传关系密切,百粒重5.01~10.0g和超过10.0g的半野生大豆组遗传关系密切。大粒野生大豆在遗传上与半野生大豆类型密切。从小粒野生大豆到大粒半野生大豆各类型的遗传分化与它们的百粒重大小有密切关联,即使与小粒秣食豆的百粒重相重叠甚至超过小粒秣食豆的半野生大豆都与小粒栽培大豆有显著的遗传差异。我们所获得的结果清楚地表明:半野生大豆属于野生种内的变异而非栽培种内变异。百粒重大小可以当作评价野生大豆物种内的遗传分化或进化程度的主要指标之一有其遗传上的理论依据。     

Genetic polymorphisms in Japanese fragrant landraces and novel fragrant allele domesticated in northern Japan

Rice fragrance is an important characteristic for Southeast Asian consumers, and fragrant landraces from Japan were first recorded in the 17th century. Principal component analysis clearly showed that Japanese fragrant landraces were genetically different from non-Japanese fragrant landraces. Japanese fragrant landraces were composed of six clades, none of which carried the most common fragrance mutation, an 8-bp deletion in exon 7 of Badh2. Fragrant landraces comprised two major groups carrying different Badh2 mutations. One group carried a known SNP at exon13 and the other a SNP at the exon1-intron1 junction as splicing donor site. The latter was considered to be a potential splicing mutant group as a novel allele at Badh2. Heterozygosity (He) scores in the two fragrant groups were not significantly different from non-fragrant landraces and modern cultivars. However, lower He scores were found around the Badh2 locus in the two groups. The potential splicing mutant group showed a more extended haplotype than the E13 SNP group. A likely causal factor responsible for loss of function is a novel splicing mutation allele that may have been generated quite recently. The fragrance allele has dispersed as a result of out-crossing under local environmental conditions.     

Genetic diversity analysis of Moroccan lentil (Lens culinaris Medik.) landraces using Simple Sequence Repeat and Amplified Fragment Length Polymorphisms reveals functional adaptation towards agro‐environmental origins

In the absence of previous molecular characterization, we assessed genetic diversity of 53 Moroccan lentil landraces including two local cultivars using simple sequence repeat (SSR) and amplified fragment length polymorphisms (AFLP). Nineteen SSRs yielded 213 alleles, and seven AFLP primer combinations gave 766 fragments of which 422 were polymorphic. Moderate to high genetic variation was observed. Several small groups of landraces were differentiated. Interestingly, one of the smallest groups contained short‐cycle landraces with high early vegetative growth. Landraces in that group were from the dry land location of Abda, where they were likely selected for adaptation to drought and heat stress over centuries. Another group contained two landraces from highland areas that may have been selected for specific adaptation to cold stress. A third group contained one landrace from the Zear region known for its seed quality and has been proposed for the protected designation of origin (PDO) quality mark. Both techniques gave evidence of differentiation of the latter landrace supporting the idea of PDO attribution. Functional grouping according to agro‐environmental origins, cycle duration and early vegetative vigour was observed.     

Diversification and genetic differentiation of cultivated melon inferred from sequence polymorphism in the chloroplast genome

Molecular analysis encouraged discovery of genetic diversity and relationships of cultivated melon (Cucumis melo L.). We sequenced nine inter- and intra-genic regions of the chloroplast genome, about 5500 bp, using 60 melon accessions and six reference accessions of wild species of Cucumis to show intra-specific variation of the chloroplast genome. Sequence polymorphisms were detected among melon accessions and other Cucumis species, indicating intra-specific diversification of the chloroplast genome. Melon accessions were classified into three subclusters by cytoplasm type and then into 12 subgroups. Geographical origin and seed size also differed between the three subclusters. Subcluster Ia contained small-seed melon from Southern Africa and South and East Asia and subcluster Ib mainly consisted of large-seed melon from northern Africa, Europe and USA. Melon accessions of subcluster Ic were only found in West, Central and Southern Africa. Our results indicated that European melon groups and Asian melon groups diversified independently and shared the same maternal lineage with northern African large-seed melon and Southern African small-seed melon, respectively. Cultivated melon of subcluster Ic may have been domesticated independently in Africa. The presence of 11 cytoplasm types in Africa strongly supported African origin of cultivated melon and indicated the importance of germplasm from Africa.     

Random amplified polymorphic DNA (RAPD) markers variability among cultivars and landraces of common beans (Phaseolus vulgaris L.) of south-Brazil

To evaluate the variability among cultivars and landraces of common bean(Phaseolus vulgaris L.), 15 cultivars and 18 landraces of common bean (Phaseolus vulgarisL.), a undefined species of Phaseolus,two landraces of Vigna angularis L., and a landrace of soybean (Glycine maxL.), were screened with fifteen oligonucleotide primers in PCR reactions. An average of 20.3 RAPD bands were scored per primer. A total of 304 amplification products were scored of which 88.8% were polymorphic among Phaseolus genotypes. Based on the RAPD markers, four major clusters were formed. Three clusters corresponded to the soybean, to the two Vigna angularis landraces, and to the Phaseolus sp. landrace, respectively. The fourth cluster include all the landraces and cultivars of Phaseolus vulgaris. This large group could be separated into three subgroups that were correlated with the phaseolin patterns and the average seed weight of the genotypes. The analysis shows that most of the landraces collected in South Brazil (17 out of 18) belong to the Andean gene pool, and most of the cultivars (13 out of 15) belong to the Middle American gene pool. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic variation among lentil (Lens culinaris Medik) landraces from Southeast Turkey

The molecular characterization of cultivated plant genepools is of foremost importance for germplasm utilization in plant breeding. However, no comprehensive genetic fingerprinting of Turkish lentil landraces existed so far. To overcome this gap, 38 lentil landraces from southeast Turkey, together with six commercial varieties, were molecularly characterized using inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) molecular markers. The ISSR analysis, performed with 14 primers, yielded 105 polymorphic bands and the AFLP analysis, carried out with six primer combinations, amplified 119 polymorphic fragments. Even though the AFLP produced more bands per primer combinations, the ISSR detected more polymorphisms. Unweighted pair-group method with arithmetic means dendrograms based on Jaccard similarities obtained from three data sets: (i) ISSR, (ii) AFLP and (iii) combined ISSR and AFLP data, were similar and separated the landraces into two main groups. Turkish lentil landraces exhibited considerable genetic diversity. One landrace from Karacadag/Diyarbakir region was significantly different from the rest of the germplasm analysed. Jaccard distances highlighted sharp differences among landraces over short geographic distances. The knowledge of regional differentiation has practical utility in the management of germplasm and in breeding programmes.     

Genetic diversity of the black gram [Vigna mungo (L.) Hepper] gene pool as revealed by SSR markers

In this study, 520 cultivated and 14 wild accessions of black gram (Vigna mungo (L.) Hepper) were assessed for diversity using 22 SSR markers. Totally, 199 alleles were detected with a mean of 9.05 alleles per locus. Wild black gram showed higher gene diversity than cultivated black gram. Gene diversity of cultivated accessions among regions was comparable, while allelic richness of South Asia was higher than that of other regions. 78.67% of the wild gene diversity presented in cultivated accessions, indicating that the domestication bottleneck effect in black gram is relatively low. Genetic distance analysis revealed that cultivated black gram was more closely related to wild black gram from South Asia than that from Southeast Asia. STRUCTURE, principal coordinate and neighbor-joining analyses consistently revealed that 534 black gram accessions were grouped into three major subpopulations. The analyses also revealed that cultivated black gram from South Asia was genetically distinct from that from West Asia. Comparison by SSR analysis with other closely related Vigna species, including mungbean, azuki bean, and rice bean, revealed that level of gene diversity of black gram is comparable to that of mungbean and rice bean but lower than that of azuki bean.     

中国栽培和野生大豆豆腐与豆乳得率的遗传变异

我国不同生态区大豆种质豆腐与豆乳得率的遗传变异是专用型品种选育的基础。以来自各生态区的564份地方品种、101份育成品种、193份野生大豆加上88份国外品种,合计946份大豆种质为材料,采用小样品定量分析技术,测定干豆腐与干豆乳得率,研究其遗传变异。结果表明,全国野生大豆和栽培大豆的干豆腐与干豆乳得率均存在很大变异,干豆腐得率变幅分别为25.32~69.59、25.52~85.89 g 100 g^-1,干豆乳得率变幅分别为40.75~82.86、39.05~91.86 g 100 g-1,栽培大豆两者的得率在野生豆基础上均有较大幅度改进;各生态区均存在与全国相同的变异情况,区内变异大于区间变异,但南方一些生态区栽培种豆腐(乳)得率变异程度相对较大,高得率材料相对较多,因本底（野生种）得率与地理纬度无关,推测与各地区栽培大豆利用方向的不同有关而形成了栽培种微弱的地理相关性;栽培材料中2.75%干豆腐得率超过75 g 100 g^-1,5.50%干豆乳得率超过85 g 100 g^-1,从中优选出来自Ⅱ、Ⅲ、Ⅳ、Ⅵ生态区的双高种质14份,可供各地区豆腐(乳)育种利用。     

Landraces: A review of definitions and classifications

The first reference to landraces as genetic resources dates from 1890. Some 20 years later the first definitions of a landrace were published. In the period 1909–1952 several definitions of the term landrace have been presented. No definitions were discovered in articles published in the period 1953–1974. The reason could be that after the Second World War attention of plant breeders and others was focussed on making instant progress. New definitions have been presented since 1974. Genetically related landraces form a landrace group. Synonyms of the term landrace and landrace group as cited in the literature are also given. The classification of types of landraces given by Mayr in 1934 had been discussed and an amended classification provided, paying attention to contamination caused by seed change. As a landrace has a complex and indefinable nature an all-embracing definition cannot be given. However, I suggest the following: an autochthonous landrace is a variety with a high capacity to tolerate biotic and abiotic stress, resulting in a high yield stability and an intermediate yield level under a low input agricultural system. This revised version was published online in August 2006 with corrections to the Cover Date.     

Variation between and within Ethiopian barley landraces

Up to 100 single plant derived lines of 18 barley landraces, collected from 18 localities of six barley growing regions of Ethiopia were studied for two years at Holetta, Ethiopia for variation in five quantitative traits; scald severity, earliness, plant height, 1000 grain weight, and leafiness. The relative latent period in the adult plant stage to barley leaf rust, a good measure for partial resistance, was assessed on the landrace lines at Wageningen, The Netherlands. The observed variation between and within landraces was very large for all traits. The magnitude of variation was so large that most, if not all, plants within a landrace had a different genotype. The landraces also varied in the degree of variation. Some landraces, 1726 and 3288 for instance, were more variable for most or all traits than other landraces such as 208925 and 212938. Days to heading and scald severity were significantly (P = 0.01) correlated with altitude, r being 0.66 and - 0.65, respectively. Resistance to scald and leafiness also increased with altitude. On average landraces became later, more resistant to scald and more leafy the higher the altitude of collection. This associated complex of traits could be an adaptation to the wetter and cooler conditions at higher altitudes. This revised version was published online in July 2006 with corrections to the Cover Date.     

Taxonomy of Portuguese Tronchuda cabbage and Galega kale landraces using morphological characters,nuclear RFLPs,and isozyme analysis: A review

Summary Morphological characters, nuclear RFLPs, and isozyme analysis were used to study the similarity between 32 Portuguese Tronchuda cabbage and Galega kale landraces, and some cabbage cultivars traditionally grown in Portugal. Forty-six morphological characters observed in two consecutive years, RFLP data from 55 nuclear probes, detecting 291 polymorphic nuclear DNA restriction fragments, and allelic frequencies in 21 putative loci, generated by nine isozymes, were analyzed by the unweighted pair group method, using arithmetic averages (UPGMA), in order to present the results in the form of a phenogram. The three methods resulted in different clustering patterns of the 32 cole accessions. Morphological characters gave consistent clustering according to the traditional landrace definition and denomination, producing clear separation between Tronchuda cabbages and Galega kales. RFLPs were unable to separate Tronchuda cabbages from Galega kales and defined five landrace groups corresponding to their geographic origins rather than to their morphological similarities. Isozymes showed poor accession discrimination and an intermediate clustering pattern with some accessions being clustered according to their geographic origins and others according to their morphological similarities. Portuguese Tronchuda cabbages and Galega kales constitute a distinct and relatively homogenous group within Brassica oleracea, sharing the same genetic background. It is concluded that Portuguese coles have evolved independently from a common ancestor to the present cultivated forms. Portugal should be considered as an important region of domestication of specialized leafy coles.     

Spanish barley landraces outperform modern cultivars at low‐productivity sites

Barley landraces from the western Mediterranean area have not been thoroughly exploited by modern breeding. This study aims at assessing the agronomic value of a core collection of lines derived from landraces of Spanish origin and to compare them with sets of successful old and modern cultivars. The agronomic performance of a set of 175 barley genotypes, comprising 159 landrace‐derived lines and 26 cultivars, was evaluated in a series of 10 field trials, carried out over 3 years and several locations. The most relevant trait of the landraces was higher grain yield at low production sites than cultivars, which may be related with better ability to fill the grain under stressful conditions. On the other hand, lateness, excessive plant height and lodging were negative traits frequently found in the landraces. Large genotype‐by‐environment interaction (GEI) for grain yield was detected, related partly with differences between germplasm groups, probably indicating local adaptation. GEI was also associated with the interaction of heading time and powdery mildew resistance with temperature.     

贵州禾落粒性基因qSH1调控区SNP分析

贵州禾是在贵州省黔东南地区种植的一类特殊的稻种,为探究其遗传特性,本研究对49份贵州禾和来源中国11个省市(自治区)和韩日的112份稻种的落粒性基因qSH1调节区序列进行测序分析.结果 表明,161份供试品种在696个碱基序列上存在13个变异位点,归为6种DNA单倍型,在功能位点12 290上,仅H6为T,属不易落粒单...     

NaCl胁迫下玉米地方品种的种子萌发效应

采用室内培养和检测,以5个玉米地方品种为材料,设置高盐(NaCl)和自来水2种处理,研究不同玉米地方品种在盐胁迫下的种子萌发和生理特性变化.结果表明,盐胁迫对玉米地方品种的种子萌发和生理有不同程度的影响,不同玉米地方品种的耐盐性存在明显的基因型差异.总体而言,不同地方品种的同一形态性状和同一地方品种的不同形态性状的耐盐胁迫指数存在差异.综合评价盐胁迫下5个玉米地方品种的耐盐特性,"DP44"是耐盐性强的品种,可作为耐盐种质加以选择,而"DP21"的耐盐胁迫能力较差.此外,对玉米品种进行耐盐胁迫的遗传改良是可行的.     

Root Phenotyping For Drought Tolerance in Bean Landraces From Calabria (Italy)

Common bean (Phaseolus vulgaris) is cultivated throughout Latin America and Africa, and for the European community, in Italy and Spain, areas are mainly subjected to drought stress which is predict to worsen by regional climatic models. The aims of this work were to identify the drought‐tolerant and drought‐sensitive bean landraces using drought tolerance and phenotypic plasticity indexes and to dissect the root morphological and 2D‐architecture traits related to drought tolerance. Thirty‐one landraces from diverse gene pools and areas of the Calabria region (South Italy), with different habits and morphological traits, were screened for drought tolerance in a hydroponic system. Root phenotyping was conducted by image analysis. Drought tolerance screening identified two landraces as drought tolerant and sensitive, respectively. Under drought stress, the drought‐tolerant landrace exhibited several interesting root traits such as a higher root length, surface area and, above all, the fineness of the whole root systems and, with emphasis, of the higher order roots. Drought stress induced plastic root responses in both bean landraces but with contrasting patterns. The drought‐tolerant landrace exhibited a dimorphic‐rooted strategy, which could be included in future utility for bean breeding programmes in drought‐prone environments.     

DNA profiling and genetic diversity of Korean soybean (<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merrill) landraces by SSR markers

Approximately 7,000 accessions of Korean soybean (Glycine max (L.) Merrill) landraces, largely composed of three collections, the Korea Atomic Energy Research Institute’s soybean (KAS), the Korean Crop Experiment Station’s soybean (KLS) and the Korean Agricultural Development and Technology Center’s soybean (KADTC) collections, have been conserved at the Rural Development Administration (RDA) genebank in Korea. The accessions within collections were classified based on their traditional uses such as sauce soybean (SA), sprouted soybean (SP), soybean for cooking with rice (SCR), and OTHERS. A total of 2,758 accessions of Korean soybean landraces were used to profile and to evaluate genetic structure using six SSR loci. A total of 110 alleles were revealed by at the six SSR loci. The number of alleles per SSR locus ranged from 9 to 39 in Satt187 and Satt_074, respectively. The number of alleles ranged from 87 in the KADTC collection to 96 in the KLS collection, and from 63 in the SCR group to 95 in the SP group. Nei’s average genetic diversity ranged from 0.68 to 0.70 across three collections, and 0.64 to 0.69 across the usage groups. The average between-group differentiation (G _st) was 0.9 among collections, and 4.1 among the usage groups. The similar average diversity among three collections implies that the genetic background of the three collections was quite similar or that there were a large number of duplicate accessions in three collections. The selection from the four groups classified based upon usage may be a useful way to select accessions for developing a Korean soybean landrace core collection at the RDA genebank. DNA profile information of accessions will provide indications of redundancies or omissions and aid in managing the soybean collection held at the RDA genebank. The information on diversity analysis could help to enlarge the genetic diversity of materials in breeding programs and could be used to develop a core collection.