Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

Genetic diversity was studied among 21 accessions of lentil using SSR markers and morphological traits in order to assess the diversification of Indian gene-pool of lentil through introgression of exotic genes and introduction of germplasm. Among these , 16 genotypes either had ‘Precoz’ gene, an Argentine line in their pedigree or genes from introduced lines from ICARDA. Sixty five SSR markers and eight phenotypic traits were used to analyse the level of genetic diversity in these genotypes. Forty three SSR markers (66 %) were polymorphic and generated a total of 177 alleles with an average of 4.1 alleles per SSR marker. Alleles per marker ranged from 2 to 6. The polymorphic information content ranged 0.33 to 0.80 with an average of 0.57, suggesting that SSR markers are highly polymorphic among the studied genotypes. Genetic dissimilarity based a dendrogram grouped these accessions into two main clusters (cluster I and cluster II) and it ranged 33 % to 71 %, suggesting high level of genetic diversity among the genotypes. First three components of PCA based morphological traits explained higher variance (95.6 %) compared to PCA components based on SSR markers (42.7 %) of total genetic variance. Thus, more diversity was observed for morphological traits and genotypes in each cluster and sub-cluster showed a range of variability for seed size, earliness, pods/plant and plant height. Molecular and phenotypic diversity analysis thus suggested that use of germplasm of exotic lines have diversified the genetic base of lentil germplasm in India. This diversified gene-pool will be very useful in the development of improved varieties of lentil in order to address the effect of climate change, to adapt in new cropping systems niches such as mixed cropping, relay cropping, etc. and to meet consumers’ preference.     

Genetic diversity in basmati rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) germplasm as revealed by microsatellite (SSR) markers

Genetic diversity among rice genotypes, including 15 indica basmati advance lines and 5 basmati improved varieties were investigated by 28 SSR markers including one indel marker. The SSRs covered all the 12 chromosomes that distributed across the rice genomes. The mean number of alleles per locus was 3.60, showing average number of polymorphism information content was 0.48. A total of 101 alleles were also identified from the microsatellite marker loci. A number of SSR markers were also identified that could be utilized to differentiate between rice genotypes. Pair wise Nei’s genetic distance between rice genotypes ranged from 0.07 to 0.95. The dendrogram based on cluster analysis by using SSR polymorphism that grouped the 20 genotypes of rice in to five clusters based on their genetic similarity. The result could be useful for the identification and selection of the diverse genotypes for the future cross breeding program and development of new rice varieties.     

Genetic diversity in basmati rice (Oryza sativa L.) germplasm as revealed by microsatellite (SSR) markers

Genetic diversity among rice genotypes, including 15 indica basmati advance lines and 5 basmati improved varieties were investigated by 28 SSR markets including one indel marker. The SSRs covered all the 12 chromosomes that distributed across the rice genomes. The mean number of alleles per locus was 3.60, showing average number of polymorphism information content was 0.48. A total of 101 alleles were also identified from the microsatellite marker loci. A number of SSR markers were also identified that could be utilized to differentiate between rice genotypes. Pair wise Nei,s genetic distance between rice genotypes ranged from 0.07 to 0.95. The dendrogram based on cluster analysis by using SSR polymorphism that grouped the 20 genotypes of rice in to five clusters based on their genetic similarity. The result could be useful for the identification and selection of the diverse genotypes for the future cross breeding program and development of new rice varieties.     

Automated sizing of fluorescent-labeled simple sequence repeat (SSR) markers to assay genetic variation in soybean

 Simple Sequence Repeat (SSR) allele sizing provides a useful tool for genotype identification, pedigree analysis, and for estimating genetic distance between organisms. Soybean [Glycine max (L.) Merr.] cultivars are identified for Plant Variety Protection (PVP) purposes by standard pigmentation and morphological traits. However, many commercial soybeans arise from a limited number of elite lines and are often indistinguishable based on these traits. A system based on SSR markers would provide unique DNA profiles of cultivars. Fluorescent labeling of alleles combined with automated sizing with internal size standards in each gel lane was used as an alternative to standard [³²P] labeling to assess genetic variability in soybean. Allelic frequencies at 20 SSR loci were determined in 35 soybean genotypes that account for greater than 95% of the alleles in North American soybean cultivars based upon pedigree analysis. An average of 10.1 alleles per locus (range: 5–17), with a mean gene diversity of 0.80 (range: 0.50 to 0.87) were observed at the 20 SSR loci. The 20 loci successfully distinguished modern soybean cultivars that are identical for morphological and pigmentation traits, as well as 7 soybean genotypes reported to be indistinguishable using 17 RFLP probes. Pedigrees of 7 cultivars were studied to estimate stability of SSRs in soybean across generations. Of the 7 pedigrees 6 had one locus in the progeny with an allele(s) that was not present in either parent. These new alleles are most likely the result of mutation. The mutation rate of SSR alleles in soybean was similar to that reported in humans. To avoid difficulty associated with mutation, DNA fingerprint data should be determined from the bulk of 30-50 plants of a cultivar. Received: 24 March 1997 / Accepted: 4 April 1997     

Molecular characterization and assessment of genetic diversity of inbred lines showing variability for drought tolerance in maize

A set of 24 genotypes bred at different centres in India as well as in CIMMYT showing variability for drought tolerance were selected for molecular and morpho-physiological characterization. A set of 35 SSR markers, having genome-wide coverage, was chosen for genotyping the inbreds. These markers generated a total of 111 polymorphic alleles with an average of 3.17 alleles per locus. The minimum and maximum PIC value was 0.27 and 0.77 with a mean of 0.5. A total of 13 unique alleles were found in the 24 inbred lines. The coefficient of genetic dissimilarity ranged from 0.192 to 0.803. NJ-based tree suggested the presence of three major clusters of which, two of them had subgroups. Phenotyping of inbreds by morpho-physiological traits revealed that there was a positive relationship among root length, chlorophyll content, relative water content while anthesis-silking interval was negative relationship with all these traits. Genotyping data complemented by morpho-physiological parameters were used to identify a number of pair-wise combinations for the development of mapping population segregating for drought tolerance and potential heterotic pairs for the development of drought tolerant hybrids.     

Genetic Diversity of Early Maturing Indian Maize (Zea mays L) Inbred Lines Revealed by SSR Markers

A set of 16 popular inbred lines, (8 released and 8 experimental) were analyzed using 24 Simple Sequence Repeats (SSR) markers. In total 71 SSR alleles were identified with a mean of 2.96 alleles per locus. The study revealed 28 rare alleles among the total, out of which 9 were unique to some of the inbred lines. The average Polymorphism Information Content (PIC) and Discrimination Rate (DR) were 0.39 and 0.61, respectively. Genetic similarity expressed as Jaccard’s coefficient varied from 0.23–0.68 with an average of 0.41. Five clusters were obtained by using Unweighted Paired Group Method using Arithmetic Averages (UPGMA). The pattern of grouping did not match well with available pedigree information, which may be attributed to inadequate pedigree information. Inbred lines used in present study revealed heterozygosity ranges from 8.3–33.3% and were clearly distinguished with a minimum set of three markers with high PIC and DR. However, fingerprints obtained using 13 markers with high DR revealed a probability of identical match by chance at 4.06×10^?8. In this study we found SSR as a good tool for characterization of maize genotypes along with morphological markers.     

Evaluation of SSR Markers for the Assessment of Genetic Diversity and Fingerprinting of Gossypium hirsutum Accessions

A total 177 simple sequence repeat (SSR) markers were screened using a set of 47 Upland cotton genotypes comprising 14 commercial varieties, 14 germplasm accessions and 19 advanced breeding lines to identify informative markers for genetic diversity assessment and fingerprinting in G. hirsutum. Only 21% (381177) of SSR markers tested showed polymorphism with a mean of 2.18 alleles per locus and with average polymorphism information content (PIC) of 0.32. The SSR markers revealed a Jaccard’ similarity coefficient ranging between 0.43 and 0.89, with an average of 0.67 among accessions. Cluster analysis using unweighted pair group method with arithmetic averages (UPGMA) and principal component analysis (PCA) indicated that majority of the genotypes were very closely related. All the 47 genotypes showed heterorygosity for at least one of the SSR loci. We discovered 19 rare and 6 unique alleles among the tested genotypes of cotton. Fingerprint based on all the 38 loci revealed a probability of identical match by chance of 3.98x10. A set of ten SSR markers was identified which could distinguish all the 47 genotypes with a moderate probability of identical match by chance (X?_D ⁿ = 0.01).     

Inheritance studies of SSR and ISSR molecular markers and phylogenetic relationship of rice genotypes resistant to tungro virus

Multivariate analyses were performed using 13 morphological traits and 13 molecular markers (10 SSRs and three ISSRs) to assess the phylogenetic relationship among tungro resistant genotypes. For morphological traits, the genotypes were grouped into six clusters, according to D² statistic and Canonical vector analysis. Plant height, days to flowering, days to maturity, panicle length, number of spikelet per panicle, number of unfilled grain per panicle and yield were important contributors to genetic divergence in 14 rice genotypes. Based on Nei's genetic distance for molecular studies, seven clusters were formed among the tungro resistant and susceptible genotypes. Mantel's test revealed a significant correlation (r = 0.834*) between the morphological and molecular data. To develop high yielding tungro resistant varieties based on both morphological and molecular analyses, crosses could be made with susceptible (BR10 and BR11) genotypes with low yielding but highly resistant genotypes, Sonahidemota, Kumragoir, Nakuchimota, Khaiyamota, Khairymota and Kachamota. The chi-square analysis for seven alleles (RM11, RM17, RM20, RM23, RM80, RM108 and RM531) of SSR and five loci (RY1, MR1, MR2, MR4 and GF5) of three ISSR markers in F₂ population of cross, BR11 × Sonahidemota, showed a good fit to the expected segregation ratio (1:2:1) for a single gene model.     

Genetic diversity analysis in sorghum germplasm as estimated by AFLP, SSR and morpho-agronomical markers

A comparison of the different methods of the estimation of genetic diversity is important to evaluate their utility as a tool in germplasm conservation and plant breeding. Amplified fragment length polymorphism (AFLP), microsatellites or SSR and morphological traits markers were used to evaluate 45 sorghum germplasm for genetic diversity assessment and discrimination power. The mean polymorphism information content (PIC) values were 0.65 (AFLPs) and 0.46 (SSRs). The average pairwise genetic distance estimates were 0.57 (morphological traits), 0.62 (AFLPs) and 0.60 (SSRs) markers data sets. The Shannon diversity index was higher for morphological traits (0.678) than AFLP (0.487) and SSR (0.539). The correlation coefficients obtained by the Mantel matrix correspondence test, which was used to compare the cophenetic matrices for the different markers, showed that estimated values of genetic relationship given for AFLP and SSR markers, as well as for morphological and SSR markers were significantly related (p <0.001). However, morphological and AFLP data showed non-significant correlation (p >0.05). Both data sets from AFLP and SSR allowed all accessions to be uniquely identified; two accessions could not be distinguished by the morphological data. In summary, AFLP and SSR markers proved to be efficient tools in assessing the genetic variability among sorghum genotypes. The patterns of variation appeared to be consistent for the three marker systems, and they can be used for designing breeding programmes, conservation of germplasm and management of sorghum genetic resources.     

Evaluation of genetic diversity of Fusarium head blight resistance in European winter wheat

Genetic diversity in relation to Fusarium head blight (FHB) resistance was investigated among 295 European winter wheat cultivars and advanced breeding lines using 47 wheat SSR markers. Twelve additional wheat lines with known FHB resistance were included as reference material. At least one SSR marker per chromosome arm, including SSR markers reported in the literature with putative associations with QTLs for FHB resistance, were assayed to give an even distribution of SSR markers across the wheat genome. A total of 404 SSR alleles were detected. The number of alleles per locus ranged from 2 to 21, with an average of 8.6 alleles. The polymorphism information content of the SSR markers ranged from 0.13 (Xwmc483) to 0.87 (Xwmc607), with an average of 0.54. Cluster analysis was performed by both genetic distance-based and model-based methods. In general, the dendrogram based on unweighted pair-group method with arithmetic averages showed similar groupings to the model-based analysis. Seven clusters were identified by the model-based method, which did not strictly correspond to geographical origin. The FHB resistance level of the wheat lines was evaluated in field trials conducted over multiple years or locations by assessing the following traits: % FHB severity, % FHB incidence, % diseased kernels, in spray inoculation trials, and % FHB spread and % wilted tips, in point inoculation trials. Association analysis between SSR markers and the FHB disease traits detected markers significantly associated with FHB resistance, including some that have not been previously reported. The percentage of variance explained by each individual marker was, however, rather low. Haplotype analysis revealed that the FHB-resistant European wheat lines do not contain the 3BS locus derived from Sumai 3. The information generated in this study will assist in the selection of parental lines in order to increase the efficiency of breeding efforts for FHB resistance.     

基于SSR标记的贵州薏苡种质资源遗传多样性?分析

利用SSR标记研究了22份薏苡种质的遗传多样性,用11对扩增带型稳定的SSR引物从供试材料中检测出105个等位基因变异,每对引物检测等位基因4～20个,平均9.55个。SSR引物的PIC介于0.3048～0.9238,平均多态性信息量为0.8255。利用UPGMA聚类分系法将供试自交系划分为4类,该划分结果与根据地理来源、种质系谱的分类结果基本一致。SSR分子标记辅助的种质改良是薏苡品种改良的重要途径。     

Microsatellite marker based genetic diversity analysis among cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis>) accessions differing for their response to drought stress

Genetic diversity is an essential input for any plant breeding programme. To assess the genetic divergence among the newly identified drought tolerant lines and elite cotton genotypes including popular varieties, a total of 51 distinctly polymorphic markers were identified after screening 142 genome-wide SSR markers. The identified polymorphic markers detected a total of 140 alleles with a mean of 2.75 alleles per loci and average polymorphism information content of 0.45. Jaccard coefficient based dissimilarity index between the genotypes ranged from 0.18 to 0.82 indicating existence of wide variation between and within the drought tolerant and susceptible genotypes at the DNA level. Cluster and factorial analyses have provided the structure of genetic diversity present and clearly distinguished the drought tolerant and susceptible cotton genotypes. Clustering pattern was in congruence with the source or pedigree of genotypes. The information generated in the present study on genetic divergence among genotypes having differential response to drought will help in selection of suitable lines as parents for developing drought tolerant cultivars in cotton. The polymorphic markers and diverse lines identified in the study will be of immense utility in molecular mapping and marker assisted breeding to achieve drought tolerance in cotton.     

Patterns of subspecies genetic diversity among oilseed <Emphasis Type="Italic">Brassica rapa</Emphasis> as revealed by agro-morphological traits and SSR markers

Brassica rapa (2n = 20, AA genome) is an important oil yielding species of the family Brassicaceae and characterized by wide range of genetic and morphological subtypes suitable for cultivation under diverse agro-climatic regions of India. In this study, genetic diversity among three subspecies of B. rapa including yellow sarson, toria and outlier brown sarson was estimated using various agro-morphological traits and simple sequence repeat (SSR) markers. Maximum variability was recorded for siliqua angle (Coefficient of variation = 30.9%), followed by seeds/siliqua (CV = 18.8%), leaf length (CV = 10%) and plant height (CV = 16.8%). Principal component analysis explained more than 50% of the total observed morphological variability for first two components. Of the 107 SSR markers tested, 80 generated reproducible, clear and distinct amplicons of which, 65 (81.25%) were found polymorphic. The number of alleles at each locus ranged from 2 to 7, with an average of 3.03 alleles per marker. A total of 197 alleles were detected at 65 SSR loci with average PIC value of 0.457 and a mean resolving power of 3.04. Neighbor-Joining cluster analysis based on morphological traits and SSR markers separately classified all the 28 genotypes into five major groups. The population structure analysis resulted into three sub-populations with certain extent of admixture among the earlier established taxonomic sub-groups. Twenty-three unique alleles were detected in thirteen B. rapa varieties. The clustering analysis and principal coordinate analysis outlined the genetic relationships among different varieties belonging to the three subspecies of B. rapa. Genetically diverse genotypes as illustrated by score plots and from the clustering patterns brought out the wide range of diversity present among B. rapa genotypes and the underlying options available for selecting parental genotypes for hybridization and developing high yielding cultivars suitable for Indian conditions.     

花生重要农艺及产量性状的全基因组关联分析

通过关联分析法发掘与花生(Arachis hypogaea)产量性状显著关联、同时又在花生基因组上随机分布的SSR位点及优异等位变异,可了解产量相关基因区域的分布特点,有助于利用分子标记辅助选择方法选育高产花生新品种。选用64个SSR标记,采用MLM(Q+K)方法对166份花生资源进行全基因组关联分析。结果表明,通过聚类分析和结构划分,供试群体受其综合性状遗传特点和来源地域的影响可被划分成7个亚群,聚类结果与群体结构基本一致,同时群体特点与材料来源地的生态划分符合同类聚集的规律。通过对6个产量相关性状的3年数值的关联分析,分别发掘出SSR位点有20个、33个和26个,2年以上重复检出的SSR位点有13个(P0.05),各SSR位点的表型变异解释率范围为0.011–0.348 1,平均为0.067 3;共检出590个等位变异,平均每个标记位点12.29个,表型变异解释率值最高的是与单株果数呈显著关联的位点TC1A02(P0.001),含21个等位变异;与产量构成主要因子紧密关联的位点中,百果重的TC1A02-C470(+41.588 5)、TC1A02-C560(+40.926 1)和p PGPseq2E6-B473(+63.953 4),单株果数的TC1A02-C500(+7.374 4),单株饱果数的GM1843-E157(+4.316 6),可用于产量性状的分子辅助育种。     

Assessing wheat (Triticum aestivum L.) genetic diversity using quality traits, amplified fragment length polymorphisms, simple sequence repeats and proteome analysis

The genetic diversity among 10 Iranian bread wheat (Triticum aestivum) genotypes was analysed using 12 quality traits, 320 amplified fragment length polymorphisms (AFLP) polymorphic fragments, 491 simple sequence repeats (SSR) alleles and 294 proteome markers. The results revealed that the genotypes differed for quality traits, AFLP, SSR and proteome markers. The average genetic diversity based on quality traits (0.684 with a range of 0.266–0.997) was higher than AFLP (0.502 with a range of 0.328–0.717), SSR (0.503 with a range of 0.409–0.595) and proteome (0.464 with a range of 0.264–0.870) markers. Although there were apparent similarities between the groupings of particular genotypes, the overall correspondence between the distance matrices appeared to be rather low. In this study, the cluster analysis based on AFLP data showed the closest agreement with genotypes’ regions of origin or pedigree information. In addition to the genetic diversity assessment, specific proteins with known function were detected uniquely for the studied genotypes. Our results suggest that the classification based on quality traits and genotypic markers of these wheat genotypes will be useful for wheat breeders to plan crosses for positive traits.     

Mapping quantitative trait loci for important agronomic traits in finger millet (<Emphasis Type="Italic">Eleusine coracana</Emphasis>) mini core collection with genomic and genic SSR markers

Allele identification for agro-morphological traits and stress resistance is a major concern across the globe for improving productivity of finger millet. Here, we used 46 genomic and 58 genic simple sequence repeats (SSRs) markers in a set of 66 accessions used to constitute a global mini-core collection for analysing their genetic structure as a population and establishing association among markers and twenty morphological traits including resistance to finger blast. Phenotypic data revealed a wide range of variation for all traits except flag leaf width and flag leaf sheath width. We got amplification of 81 alleles by the 31 genomic SSRs at an average of 2.61 alleles per locus. Polymorphism information content (PIC) values varied from 0.21 to 0.75 and average gene diversity was 0.49. Structure analysis of the population using the genomic SSR data divided the accessions into two clusters where Indian and exotic accessions were grouped in separate clusters. Genic SSRs which were associated with blast resistance genes, amplified 36 alleles at an average of 2 alleles per locus. PIC values ranged from 0.32 to 0.37 and average gene diversity was 0.45. Population structure analysis using data from these SSRs grouped the accessions into three clusters, which broadly correspond to their reaction to blast disease. Twenty-two significant associations were found using the GLM approach for 20 agro-morphological traits both in 2012 and 2014, while, 7 and 5 significant marker-trait associations were identified using MLM in 2012 and 2014 respectively. The SSR markers FMBLEST35 and FMBLEST36 designed from the Pi21 gene sequence of rice were found to be associated with blast disease resistance in finger millet indicating that the gene homologues play a significant role in an important role for neck blast resistance.     

Assessment of genetic variation among commercial tomato (Solanum lycopersicum L) varieties using SSR markers and morphological characteristics

Simple sequence repeats (SSR) is one of the most suitable markers for variety identification as it has great discrimination power for varieties with limited genetic variation. Genetic characterization of commercial tomato varieties was investigated using 33 SSR markers and 22 morphological traits. Thirty three SSR primer pairs were screened for 63 tomato varieties. A total of 132 polymorphic amplified fragments were obtained by using 33 SSR markers. The average polymorphism information content (PIC) was 0.628 ranging from 0.210 to 0.880. One hundred thirty two SSR loci were used to calculate Jaccard's distance coefficients for UPGMA cluster analysis. A clustering group of varieties, based on the results of SSR analysis, were categorized into cherry and classic fruit type varieties. Almost all of the varieties were discriminated by SSR marker genotypes. The relationship between morphological and molecular data for 33 varieties out of 63 varieties was analyzed using Mantel matrix correspondence test. The correlation value between two methods was 0.644. However, SSR based dendrogram topology showed some similar form with morphological traits at the two main groups. Therefore, these markers may be used wide range of practical application in variety identification and pre-screening for distinctiveness test of tomato varieties.     

Genetic diversity of elite sweet sorghum genotypes assessed by SSR markers

To determine genetic diversity among 47 elite sweet sorghum (Sorghum bicolor ssp. bicolor L.) genotypes, 46 simple sequence repeat (SSR) markers evenly distributed on all 10 chromosomes were selected. All SSR markers used were polymorphic among the genotypes studied. A total of 228 alleles were identified with an average of 4.96 alleles per marker. Furthermore, the genotypes studied showed medium genetic diversity. Clustering analysis grouped the 47 genotypes into 5 distinct clusters.