Comparison of molecular markers and coefficients of parentage for the analysis of genetic diversity among spring bread wheat accessions

The comparison of different methods of estimating genetic diversity could define their usefulness in plant breeding and genetic improvement programs. This study evaluates and compares the genetic diversity of 70 spring wheat accessions representing a broad genetic pool based on molecular markers and parentage relationships. The sample was composed of 32 accessions from the International Maize and Wheat Improvement Center (CIMMYT) and 38 from other breeding programs worldwide. Eight AFLP-primer combinations and 37 pairs of SSR primers were used to characterize the accessions and the Coefficients of Parentage (COP) were calculated from registered pedigrees. The average genealogical (COP) similarity (0.09 with a range of 0.0–1.0) was low in comparison to similarity calculated using SSR markers (0.41 with a range of 0.15–0.88) and AFLP markers (0.70 with a range of 0.33–0.98). Correlation between the genealogical similarity matrix (excluding accessions with COPs = 0) and the matrices of genetic similarity based on molecular markers was 0.34≤r≤0.46 (p <0.05). It is concluded that AFLP and SSR markers are generally in agreement with estimates of diversity measured using COPs, especially when complete pedigree data are available. However, markers may provide a more correct estimate due to some unrealistic assumptions made when calculating COPs, such as absence of selection. Furthermore, both COP and marker distances indicate that CIMMYT accessions are different from the worldwide group of accessions. This revised version was published online in July 2006 with corrections to the Cover Date.     

Assessment of genetic diversity in bread wheat genotypes for tolerance to drought using AFLPs and agronomic traits

Moisture stress greatly limits the productivity of wheat in many wheat-growing regions of the world. Knowledge of the degree of genetic diversity among parental materials for key selection traits will facilitate the development of high yielding, stress tolerant wheat cultivars. The objectives of this study were to: (i) use amplified fragment length polymorphisms (AFLPs) to assess genetic diversity among bread wheat lines and cultivars with different responses to drought stress in two distinct environments and, (ii) compare genetic diversity estimated by AFLPs with diversity evaluated on agronomic performance under drought stress. Twenty-eight genotypes, 14 from Iran and 14 developed or obtained by CIMMYT, were evaluated in the study. Phenotypic data on the 14 Iranian lines were obtained in Iran, and data on the 14 CIMMYT lines were collected in Mexico. Ten AFLP primer pairs detected 335 polymorphic bands among the 28 cultivars. At the 5th fusion level of the resulting dendrogram, 6 genotype clusters were identified. Thirteen of the 14 CIMMYT genotypes grouped into one cluster while 4 of the remaining groups were comprised only of Iranian genotypes. When the agronomic performance of the Iranian materials was compared with the AFLP diversity analysis, 5 of the 6 drought susceptible genotypes clustered together in the agronomic dendrogram, and were located in the same cluster in the AFLP dendrogram. However, the drought tolerant Iranian materials did not show the same degree of relationship. The CIMMYT materials did not demonstrate a significant association between agronomic performance and genetic diversity determined using AFLPs. Clearly these data show that there are genotypes with similar agronomic performance and different genetic constitutions in this study that can be combined in a breeding program to potentially improve tolerance to drought stress.     

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.     

Spanish spelt: a separate gene pool within the spelt germplasm

The renewed interest in spelt (Triticum spelta L.) for wheat improvement programmes requires the study of the available genetic diversity. The purpose of this study was to assess genetic diversity within a Spanish spelt collection. Sixty‐six Spanish spelt accessions, 19 accessions of T. spelta and T. macha from different origins, three bread wheat cultivars (T. aestivum) and one accession of T. dicoccum were screened using simple sequence repeats (SSRs). The diversity observed within the Spanish group was comparable with that observed in the other wheat varieties, despite their broader geographical diversity. Indeed, the highest polymorphic information content value calculated with SSRs for Spanish material (0.90) is similar to that observed for the other wheat varieties (0.98). Principal component analysis explained 46.5% of the cumulative variation and confirmed the Spanish accessions as a separate group. This study showed the Spanish spelt collection to be a variable and unique genetic resource for wheat and spelt breeding programmes.     

Genetic diversity in cornsalad (Valerianella locusta) and related species as determined by AFLP markers

Fifteen amplified fragment length polymorphism (AFLP) EcoRI/MseI‐based primer combinations with five selective bases (Eco RI‐ANN, MseI‐CN) were used to estimate genetic diversity among 45 line varieties of cultivated cornsalad and 19 genebank accessions classified into nine different species related to cornsalad. Polymorphic fragments were scored for calculation of Jaccard's coefficient of genetic similarity (GS). The average GS estimate in elite germplasm (GS = 0.90) was substantially higher than in exotic germplasm (GS = 0.47). UPGMA‐cluster analysis revealed genetic relationships among recently bred varieties, old varieties and genebank accessions. Analysis of molecular variance indicated almost threefold variability within sets compared with between sets due to a high level of polymorphism among wild species. Sources for increasing genetic diversity in elite germplasm of cornsalad were suggested and a duplicate among the genebank accessions was detected. AFLPs could be considered a powerful tool for genetic diversity estimation in cornsalad germplasm and are recommended for systematic fingerprinting of remaining cornsalad species.     

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.     

High genetic diversity of Spanish common wheats as judged from gliadin alleles

Gliadin alleles were identified in 100 common wheat cultivars registered and/or grown in Spain during the last 40 years. A very high level of genetic polymorphism was found: in total, 103 allelic variants including one null‐allele were found at the six major Gli loci in the Spanish wheats studied. An average genetic diversity for these six loci was found to be higher (H=0.844) than in any group of wheat cultivars studied previously. Spanish wheats bred in Spain demonstrated even higher genetic diversity (H=0.868), probably because of the occurrence in this group of some landraces (local varieties) assumed to be strongly differentiated to fit local environments. The high level of genetic diversity of wheats grown in Spain was maintained by the introduction of distantly related wheat germplasm from different sources, especially from Italy and CIMMYT. A slight decrease of genetic diversity in recently registered cultivars might be caused by the excessive introduction of French wheats. Thirteen new alleles found in Spanish wheats were catalogued, including Gli‐D2w which encodes the first Gli‐D2‐controlledγ‐gliadin to be found.     

Genetic relationships and diversity among Tibetan wheat, common wheat and European spelt wheat revealed by RAPD markers

An endemic hexaploid wheat found in Tibet, China was taxonomically classified as a subspecies in common wheat, i.e. Triticum aestivum ssp. tibetanum. Seven accessions of the Tibetan wheat, 22 cultivars of common wheat and 17 lines of spelt wheat were used for RAPD analysis to study the genetic relationships of the Tibetan wheat with common wheat and spelt wheat, and to assess the genetic diversity (GD) among and within the taxa. RAPD polymorphism was found to be much higher within spelt wheat and the Tibetan wheat than within common wheat. The GD value between the Tibetan wheat and common wheat is lower than that between the Tibetan wheat and spelt wheat. The result of cluster analysis showed that the 46 genotypes were distinctly classified into two groups. Group 1 included all European spelt wheat lines, while group 2 includes all Chinese common wheat and the Tibetan wheat accessions. However, the Tibetan wheat was substantially differentiated from Chinese common wheat at a lower hierarchy. Our results support an earlier classification of the Tibetan wheat as a subspecies in common wheat. European spelt wheat and the Tibetan wheat showed much higher genetic diversity than Chinese common wheat, which could be used to diversify the genetic basis for common wheat breeding. This revised version was published online in July 2006 with corrections to the Cover Date.     

利用关联分析发掘小麦自然群体旗叶叶绿素含量的优异等位变异

为揭示小麦自然群体干旱胁迫条件下旗叶叶绿素含量的变化, 筛选相关标记的优异等位变异, 以262份小麦种质资源组成的自然群体为材料, 分别种植在北京的2个试验地点, 均设雨养和灌溉处理, 于开花期和灌浆期检测旗叶叶绿素含量。以分布于21条染色体的169个SSR标记检测所有材料的基因型, 利用STRUCTURE 2.3.2软件分析群体结构, 用TASSEL软件的MLM (mixed linear model)方法对小麦自然群体的旗叶叶绿素含量进行关联分析。在此基础上, 将携带某等位变异的所有材料表型均值与携带无效等位基因(null allele)材料表型均值比较, 估计等位变异的表型效应, 鉴别优异等位变异。共检测到2048个等位变异, 每位点2~37个等位变异, 平均12个。每位点的标记多态性信息量(PIC)为0.008~0.936, 平均0.628。在22个标记位点共检测出40个(次)与旗叶叶绿素含量极显著的关联, 其中11个标记位点有2次以上的关联, Xwmc419-1B和Xgwm501-2B分别有3次关联。在Xcfa2123-7A、Xgwm232- 1D和Xgwm429-2B位点分别检测到效应值大于4.0的等位变异。     

Assessing diversity in Triticum durum cultivars and breeding lines for high versus low cadmium content in seeds using the CAPS marker usw47

Cadmium (Cd) is a toxic heavy metal that occurs naturally in soils. Durum wheat is known to accumulate generally more Cd than other cereal crops. The uptake of Cd in durum wheat is governed by the gene Cdu1, which co‐segregates with several DNA markers, such as the co‐dominant marker usw47 and the dominant marker ScOPC20. A panel of 314 durum wheat cultivars or lines originating from 16 countries or regions were assessed with usw47. The plant material was mainly comprised of cultivars and modern breeding lines. From this set, 165 durum wheat lines were classified as low‐Cd accumulators, 144 high‐Cd accumulators and five were heterogeneous. A smaller subset of 16 cultivars had previously been evaluated for Cd accumulation in replicated field trials. Lines with the high‐Cd allele showed a 2.4‐fold higher Cd content in the seeds than lines with the low‐Cd allele. We also compared the utility of markers usw47 and ScOPC20 as selection tools. Marker‐assisted selection appears as a robust and practicable tool for breeding durum cultivars with low‐Cd content.     

Pattern analysis on grain yield performance of Chinese and CIMMYT spring wheat cultivars sown in China and CIMMYT

Understanding the relationships among testing environments is essential for better targeting cultivars to production environments. To identify patterns of cultivar, environment, cultivar-by-environment interactions, and opportunities for indirect selection for grain yield, a set of 25 spring wheat cultivars from China and the International Maize and Wheat Improvement Center (CIMMYT) was evaluated in nine environments in China and four management environments at CIMMYT in Cd. Obregon, Mexico, during two wheat seasons. Genetic background and original environment were the main factors influencing grain yield performance of the cultivars. Baviacora M 92, Xinchun 2 and Xinchun 6 showed relatively more stable and higher grain yields, whereas highly photoperiod sensitive cultivars Xinkehan 9, Kefeng 6 and Longmai 19 proved consistently inferior across environments, except in Harbin and Keshan, the two high latitude environments. Longmai 26, also from high latitude environments in the north-eastern Heilongjiang province, was however probably not as photoperiodicly sensitive as other cultivars from that region, and produced much higher grain yield and expressed a broader adaptation. None of the environments reported major diseases. Pattern analyses revealed that photoperiod response and planting option on beds were the two main factors underlying the observed interactions for grain yield. The production environment of planting on the flat in Mexico grouped together with Huhhot and Urumqi in both wheat seasons, indicating an indirect response to selection for grain yield in this CIMMYT managed environment could benefit the two Chinese environments. Both the environment of planting on the flat with Chinese Hejin and Yongning, and the three CIMMYT environments planting on raised beds with Chinese Yongning grouped together only in one season, showing that repeatability may not be stable in this case.     

Genetic diversity and differentiation of Chinese wild soybean germplasm (G. soja Sieb. & Zucc.) in geographical scale revealed by SSR markers

Wild soybean (Glycine soja), as the progenitor of soybeans (G. max), is widely distributed in China and has been collected as a supplementary germplasm pool of soybeans. In this study, 375 wild soybean accessions from a set of genebank core collection were analysed for genetic diversity by using 42 simple sequence repeat primer pairs. The mean allele number per locus was 19.62. Ten‐percent unique alleles involving 35 or 83.33% loci differentiated among the geographical regions. The mean gene diversity (h) per locus was 0.89. A very low mean coefficient of gene differentiation (G_ST = 0.08) for geographical regions and a high mean within‐region gene diversity (H_S = 0.81) were observed, indicating that most genetic diversity existed within the regions. There was an obvious relationship between genetic distance and geographical distance. The results showed multiple centers of genetic diversity for Chinese wild soybean in North China, the Huanghe River Valley, and Central China as well as the Changjiang River Valley, implicating multiple site origins of soybeans within China.     

S‐locus diversity and cross‐compatibility of wild Prunus avium for timber breeding

Prunus avium is primarily cultivated for its fruit, sweet cherries. However, it is also used to produce high‐quality timber. In a P. avium seed orchard, gametophytic self‐incompatibility is a restriction for free pollen flow and should be considered when establishing basic forest materials. In this study, S‐locus diversity and cross‐incompatibility of wild cherry individuals in clonal banks established for breeding for timber production were investigated. Wild cherry trees (140) with outstanding forest growth habit, collected in northern Spain, grafted and planted in two clonal banks, were genotyped at the S‐locus. The self‐incompatibility S‐locus genes, S‐RNase and SFB, were analysed by PCR. Twenty‐two S‐haplotypes, resulting in 72 different S‐genotypes, were identified. The genotypes were grouped into 33 incompatibility groups and 39 unique genotypes. This initial S‐locus analysis revealed large genetic diversity of wild cherry trees from the Spanish northern deciduous forest, and provides useful information for seed orchard design. Wild P. avium displays significantly more genetic diversity than what is detected in local cultivars, revealing a narrowing of genetic diversity during local domestication.     

Genetic diversity and population structure of ‘Khao Kai Noi’, a Lao rice (Oryza sativa L.) landrace,revealed by microsatellite DNA markers

Rice (Oryza sativa L.) is the main food for people in Laos, where it has been grown and eaten since prehistory. Diverse landraces are grown in Laos. ‘Khao Kai Noi’, a landrace favored for its eating quality, is held in the nationwide collection of traditional landraces in the Lao national genebank. Genetic diversity is crucial for sustainable use of genetic resources and conservation. To investigate the genetic diversity of ‘Khao Kai Noi’ for conservation, we genotyped 70 accessions by using 23 polymorphic simple sequence repeat markers. The markers generated 2 to 17 alleles (132 in total), with an average of 5.7 per locus. The total expected heterozygosity over all ‘Khao Kai Noi’ accessions was 0.271. Genetic variation was largest among accessions and smallest within accessions. Khao Kai Noi accessions were classified into three different genetic backgrounds, but there was unclear association between the three inferred population and name subgroups and geographical distribution. Most of the accessions were clustered with temperate japonica and showed genetic relatedness to rice from neighboring provinces of Vietnam, suggesting a Vietnamese origin. The results of this study will contribute to the conservation, core collection and future breeding of the Khao Kai Noi population.     

Regional patterns of microsatellite diversity in Ethiopian tetraploid wheat accessions

This study was conducted to assess regional patterns of diversity of Ethiopian tetraploid wheat accessions and to identify areas of diversity that can be used as source of new germplasm for developing high yielding and stable varieties. A collection of 133 Ethiopian tetraploid wheat accessions and eight introduced cultivars was analysed using 29 wheat microsatellite markers. A total of 383 alleles were detected with an average value of 13.14 alleles per locus. Relatively more alleles were observed in the B genome than in the A genome. Gene diversity indices ranged from 0.08 to 0.95, with a mean value of 0.72. Accessions collected from the same region were pooled and the number of alleles and gene diversity were calculated over the 29 simple sequence repeats for each region. Higher numbers of alleles were detected in the Shewa region (8.72), followed by Tigray (5.86) and Hararghe (5.76). The highest average gene diversity value was found in Shewa (0.65), followed by Gondar (0.64). No significant correlation was observed between geographic distance and genetic distance. Out of 383 different alleles detected, 93 (24.4%) were observed to be region‐specific. Region‐specific alleles were found across all chromosomes except for Xgwm752, Xgwm155 and Xgwm148. Genetic similarity coefficients were estimated for all the possible 55 pairs of regional comparisons and they ranged from 0.16 to 0.52, with a mean value of 0.50. All provinces were differentiated in the UPGMA cluster diagram.     

High‐throughput development of SSR marker candidates and their chromosomal assignment in rye (Secale cereale L.)

Shotgun survey sequences of flow‐sorted individual rye chromosomes were data mined for the presence of simple sequence repeats (SSRs). For 787,850 putative SSR loci, a total of 358,660 PCR primer pairs could be designed and 51,138 nonredundant SSR marker candidates were evaluated by in silico PCR. Of the 51,138 SSR primer candidates, 1,277 were associated with 1,125 rye gene models. A total of 2,112 of the potential SSR markers were randomly selected to represent about equal numbers for each of the rye chromosomes, and 856 SSRs were assigned to individual rye chromosomes experimentally. Potential transferability of rye SSRs to wheat and barley was of low efficiency with 4.3% (2,189) and 0.4% (223) of rye SSRs predicted to be amplified in wheat and barley, respectively. This data set of rye chromosome‐specific SSR markers will be useful for the specific detection of rye chromatin introgressed into wheat as well as for low‐cost genetic and physical mapping in rye without the need for high‐tech equipment.     

Development of chloroplast‐specific microsatellite markers for molecular characterization of alloplasmic lines and phylogenetic analysis in wheat

Wheat (Triticum aestivum L.) is strictly a self‐pollinated crop, where hybrid breeding requires well‐characterized cytoplasmic male sterile (CMS) lines. The CMS has mostly been developed by substituting nuclear genome of wheat into the cytoplasm from wild relatives. Molecular characterization of 90 genotypes including 82 CMS lines originating from five different species, namely Aegilops speltoides, Ae. kotschyi, Ae. variabilis, Triticum araraticum and T. timopheevii, and eight popular varieties was carried out. Consequently, a set of 25 microsatellite markers specific to chloroplast (cpSSRs) were designed and successfully validated for specificity of amplification. A total of 15 cpSSRs (60%) were found polymorphic, of which three cpSSRs (TaCM7, TaCM8 and TaCM11) in genic region and twelve cpSSRs were located in intergenic region. Phylogenetic analysis of genotypes using cpSSRs revealed two major groups well in accordance with respective origin. A set of cpSSRs and phylogeny of CMS belonging to different origins developed, which will be helpful for the improvement in CMS system in wheat. The genic cpSSRs can be used for the allele mining and evolutionary studies.     

Identification of a diverse mini‐core panel of Indian rice germplasm based on genotyping using microsatellite markers

Identification of a small core germplasm set representing the available genetic diversity is essential for its proper evaluation and subsequent utilization in rice improvement programmes. For constituting a small diverse mini‐core panel of Indian rice germplasm, a representative set of 6912 accessions drawn based on their geographic origin from the whole rice germplasm collection available in the National Gene Bank was genotyped using 36 microsatellite markers. Automated fragment analysis of amplicons yielded a total of 435 alleles, with an average 12.4 and range of 3–29 alleles per locus. Polymorphism information content (PIC) ranged from 0.08 (RGNMS190) to 0.86 (RM552) with an average of 0.528. Based on genotyping data, a mini‐core consisting of 98 genotypes was identified. Ninety‐four per cent of the alleles present in the core set were present in the mini‐core. The identified small but diverse panel will be useful for further intensive trait‐specific evaluation and utilization in allele mining.     

The genetic diversity of old and modern Siberian varieties of common spring wheat as determined by microsatellite markers

The objective of this study was to assess genetic diversity within old and modern common spring wheat (Triticum aestivumL.) varieties cultivated in Siberia and to find out whether old Siberian varieties could be a potential source for genetic diversity in modern wheat breeding in Siberia. A set of 54 varieties was analysed using 22 wheat microsatellite markers (WMS), determining 23 loci located on 19 different chromosomes. In total, 151 alleles were detected with an average of 6.6, ranging from three to 11 alleles per locus. The average genetic diversity value (polymorphic information content) was 0.70. WMS located in the B genome produced more alleles per locus (7.6) compared with WMS located in the A (6.0) and D (6.0) genomes. Genetic similarity values between varieties ranged from 0.19 to 0.96 and were used to produce a dendrogram. With a few exceptions the varieties studied were clustered in two nearly equal groups consisting of predominantly old (released before 1960) and modern (released in 1960‐90s) varieties, respectively. Genetic diversity values within these two groups were similar with 0.60 and 0.58, respectively. The numbers of group‐specific alleles were 34 and 29, respectively. A significant variation in frequencies of 79 shared alleles was observed. The results obtained by using genomic microsatellite sequences demonstrated that breeding has not resulted in a decrease in the genetic diversity in Siberian spring wheat. However, significant quantitative and qualitative changes in allelic frequencies of different loci were detected. It may be suggested, that old Siberian common spring wheat varieties are a potential basis for genetic diversity in modern wheat breeding in Siberia.     

Variable resistance of bread wheat (Triticum aestivum) lines carrying 2NS/2AS translocation to wheat blast

Wheat blast disease, caused by Magnaporthe oryzae (anamorph Pyricularia oryzae), produces severe damage to wheat production in South America. It was observed that many resistant cultivars contain the 2NS/2AS translocation from Triticum ventricosum. In this study, we evaluate the presence of the 2NS/2AS translocation in 57 advanced breeding lines and one variety ‘Caninde 1’ from Paraguayan wheat germplasm, using VENTRIUP‐LN2 primers. The germplasm ‘Caninde 1 and 22’ of the breeding lines, found positive for the presence of 2NS/2AS translocation, were inoculated with a single aggressive Magnaporthe pathotype P14‐039, to assess their response to wheat blast infection under controlled conditions. Based on the disease infection score, ten of the breeding lines, ‘Caninde 1’ and ‘Milan’ (positive control), were classified as resistant. Three of the remaining breeding lines were classified as moderately resistant, five as moderately susceptible and other four as susceptible. Our results show that the expression of 2NS/2AS‐based blast resistance is more dependent on genetic background of the inserted germplasm than previously envisioned.