Genetic Diversity Of Germplasm Research Articles

Diversity in Lucerne (Medicago sativa L.) germplasm for morphology, yield and molecular markers and their correlations

Lucerne is an important legume forage grown worldwide due to its high nutritive value, yield potential, quality and survival under highly contrasting environments. Estimation of genetic diversity in germplasm is an important criterion in breeding programme and is done based on phenotypic characters, biochemical and molecular markers. Thirty one accessions of Lucerne collected from Maharashtra and Gujarat were evaluated for morphological, yield characters, molecular markers and were compared with national check RL-88. The diversity analysis of morphological and yield characters indicated wide range of variation within the accessions. The accession RLG 08-1 recorded significant differences for plant height, number of tillers per plant, internodal length, green fodder, dry matter and crude protein yield (P 0.05) over RL-88. Green fodder yield was significantly correlated with plant height (0.72**), no. of tillers per plant (0.71**) and internodal length (0.71**). Dry matter yield was found significantly correlated with plant height, no. of tillers per plant, internodal length and crude protein yield (0.70**, 0.69**, 0.70** and 0.99**). Leaf stem ratio was not linearly correlated with green fodder, dry matter and crude protein yield. Principal component analysis (PCA) demonstrated that the first two PCs contributed to 93.7% of total variance among the accessions. The accession RLG 08-1 was found superior among all the accessions. Thirteen Inter Simple Sequence Repeats (ISSRs) markers showed 82.8% polymorphism. The dendrogram revealed slight geographical structuring and RLG 08-1 was found genetically distinct from other accessions.Mantel correlation was not observed between morphological and yield characters as well as molecular markers.

Assessment of genetic diversity in germplasm of Guinea grass (Panicum maximum Jacq.)

Mucuna pruriens is a nutritionally and pharmaceutically important underutilized legume belonging to genus Mucuna of Leguminosae family. Extensive intraspecific diversity and adverse morphological features among the members have led to taxonomical confusions in the species. A total of 12 Mucuna pruriens accessions including its two botanical varieties, var. pruriens and var. utilis with six accessions each were analyzed to characterize the intraspecific diversity among them using the three barcode markers viz. ITS2, matK and trnHpsbA. Extensive intraspecific sequence diversity was observed in the trnHpsbA region, where as ITS2 and matK exhibited significant conserved regions. Such intraspecific sequence diversity is a limitation in adapting trnHpsbA as barcode as it may lead to misinterpretations, but in the present study an attempt has been made to extrapolate this diversity to explain within the species variations among Mucuna pruriens genotypes. Intraspecific sequence variations exhibited by trnHpsbA sequences were 83% in correlation with morphological features. The between groups mean distance of var. pruriens and var. utilis was found to be 0.346. Results of this study will complement with the existing molecular, morphological, ytological and biochemical markers towards Velvet bean improvement programs.

Assessment of genetic diversity in germplasm of Guinea grass (Panicum maximum Jacq.)

In the present study, sixty genotypes of Guinea grass were evaluated for assessing genetic diversity for ten different quantitative characters for exploitation in a breeding programme aimed at improving yield potential of Guinea grass by using Mahalanobis D2 statistics. The genotypes were grouped into ten clusters suggesting the presence of genetic diversity. The cluster I had maximum of 30 genotypes followed by II and III having 15 and 7 genotypes, respectively. These clusters having maximum number of genotypes, reflecting narrow genetic diversity. The inter cluster distances were greater than intra cluster distances, revealing that the selected genotypes were highly divergent. The maximum intra cluster distance was recorded for cluster III (5.63) while clusters IV, V, VI, VII and VIII and X (0.00) were solitary and showed no intra-cluster distance values. The genetically more divergent genotypes present in cluster III and IX as indicated by inter cluster distance value (21.63). Cluster VIII and Cluster V had least number of single genotype and emerged with contained highest cluster mean value for number of tillers/plant, number of leaves/plant, good leaf weight, leaf: stem ratio, green fodder yield/plant and crude protein content. Hence, GGLC 12 genotype in cluster VIII and GGLC 19 in cluster V can be successfully utilized in breeding programme for development of Guinea grass varieties with improved fodder yield and quality.

Application of genetic modification and genome editing for developing climate‐smart banana

AbstractBanana is a major staple food crop feeding more than 500 million people in tropical and subtropical countries. Its production is largely constrained by diseases and pests in addition to other factors such as declining soil fertility, narrow genetic diversity in germplasm, and inadequate availability of clean planting material. The impact of climate change, particularly a rise in temperature and drought, is predicted to affect production adversely due to direct effect on plant agronomy and also influence on pathogens, pests, and their interactions with host plants. There is need to develop climate‐smart varieties of banana with multiple and durable resistance to combat abiotic stresses such as extreme temperature and drought, and biotic stresses such as pathogens and pests. Modern breeding tools, including genetic modification and genome editing, can be applied for the improvement of banana bypassing the natural bottlenecks of traditional breeding. Intensive efforts using genetic modification have been made to develop improved banana varieties with resistance to biotic stresses; however, these need to be coupled with tolerance to abiotic stresses. Genome editing, an emerging powerful tool, can be applied for developing sustainable solutions to adapt to climate change by resisting biotic and abiotic stresses. CRISPR/Cas9‐based genome editing has been lately established for banana, paving the way for functional genomics allowing identification of genes associated with stress‐tolerant traits, which could be used for the improvement of banana for adaptation to a changing climate. This article presents an overview of recent advancements and prospective on the application of genetic modification and genome editing for developing climate‐smart banana.

Ocena genetičke raznolikosti genotipova tvrde pšenice prema karakteristikama koje je definisao UPOV

Estimation of the level of durum wheat germplasm genetic diversity is important for its classification and efficient use in breeding programmes. The aim of this study was to assess genetic diversity of durum wheat genotypes developed at the Institute of Field and Vegetable Crops in Novi Sad, Serbia, with 26 morphological characteristics based on the International Union for Protection of New Varieties of Plants guidelines. The Shannon diversity index was used as an indicator of morphological diversity and it ranged from 0.283 for glaucosity of lower side of the flag leaf blade and density of hairiness of uppermost node of the culm, to 0.950 for the ear colour, with the mean value of 0.616, indicating a medium to high level of morphological diversity. On average, the diversity was higher for traits relating to generative organs than for those associated with vegetative plant organs. The 21 morphological characteristics were sufficient to distinguish unique profiles of all durum wheat genotypes. The estimation of varietal diversity and identification of morphological characteristics with the highest discriminative power were done by multiple correspondence analysis. The traits that contributed the most to the distinction of genotypes were the ear colouration, length of beak of the lower glume, lower glume shape, ear length of awns at tip relative to ear length and colour of awns. Morphological characterization using the traits with the highest discriminative power could be a useful complementary method for durum wheat germplasm classification and diversity analysis.

Genetic diversity analysis of “<i>Murungakayan</i>” rice accessions based on seed morphology and molecular characterization

Genetic diversity of germplasm among species and within the species is important for systematic conservation of genetic resources. This study was conducted to assess the genetic diversity and to identify similar groups among the twenty-seven Murungakayan accessions conserved at the gene bank of Plant Genetic Resource Centre, Gannoruwa. Seed morphological characterization was done according to the standard descriptors for rice and data were analysed using Minitab 15.1. Molecular assessment was done using 31 SSR markers and PCR amplified products were resolved using 8% polyacrylamide gel electrophoresis. Bands were manually scored and analyzed using PowerMarker version 3.25. Morphological analysis grouped these accessions into ten clusters. The molecular analysis based on SSR markers generated 108 alleles across 27 populations. Polymorphism Information Content values ranged from 0.00 (RM 518 and RM 237) to 0.72 (RM 515) which revealed high genetic diversity. Nei’s genetic distance among accessions ranged from 0.00 to 0.9 and a dendogram grouped the accessions into eight clusters. Four sets of duplicates were identified with high genetic similarities. According to the molecular and morphological analyses, accessions 3490, 5378, 5614, 6279, 12824, 3329, 3491 and 5611 can be identified as the representative set of Murungakayan with high similarity. The results suggested that microsatellite markers along with morphological data could be used for identification of the representative set of Murungakayan accessions for systematic conservation and utilization.

Comparison among Methods and Statistical Software Packages to Analyze Germplasm Genetic Diversity by Means of Codominant Markers

Co-dominant markers’ data are often analysed as if they were dominant markers, an over-simplification that may be misleading. Addressing this, the present paper aims to provide a practical guide to the analysis of co-dominant data and selection of suitable software. An overview is provided of the computational methods and basic principles necessary for statistical analyses of co-dominant molecular markers to determine genetic diversity and molecular characterization of germplasm collections. The Hardy–Weinberg principle is at the base of statistical methods to determine genetic distance, genetic diversity, and its distribution among and within populations. Six statistical software packages named GenAlEx, GDA, Power Marker, Cervus, Arlequin, and Structure are compared and contrasted. The different software packages were selected based on: (i) The ability to analyze co-dominant data, (ii) open access software, (iii) ease of downloading, and (iv) ease of running using a Microsoft Window interface. The software packages are compared analyzing the same dataset. Differences among parameters are discussed together with the comments on some of the software outputs.

Application of genomic tools to avocado (Persea americana) breeding: SNP discovery for genotyping and germplasm characterization

Avocado (Persea americana) is an important tropical and subtropical fruit tree crop. Traditional tree breeding programs face the challenges of long generation time and significant expense in land and personnel resources. Avocado selection and breeding can be more efficient and less expensive through the development of molecular markers for the estimation of germplasm genetic diversity, marker-assisted selection (MAS), and creation of linkage maps. Two important breeding resources, the world's two largest avocado mapping populations and an extensive germplasm collection, are housed at the USDA-ARS Subtropical Horticulture Research Station (SHRS) in Miami, Florida. However, to use these resources to their greatest advantage, many thousands of genetic markers are necessary. Here, we describe the development of the first set of avocado genetic markers based on single-nucleotide polymorphism (SNP) variation in expressed genes. RNA sequencing was used both to build a reference transcriptome from 'Hass', the most widely grown avocado cultivar worldwide, and to identify SNPs by alignment of RNA sequences from the mapping population parents to the ˈHassˈ transcriptome. This study provides a new genomic tool for the avocado community that can be used to assess the genetic diversity of avocado germplasm worldwide and to optimize avocado breeding and selection programs by complementing traditional breeding methods with molecular approaches, thus increasing the efficiency of avocado genetic improvement.

Estimative of genetic diversity in germ-plasm of elephant grass using the Gower algorithm

This work aimed at estimating the genetic divergence among 85 accessions of elephant-grass using the Gower algorithm for the joint study of quantitative and qualitative traits. The experiment was conducted in the city of Campos dos Goytacazes, Rio de Janeiro state, Brazil, with of 85 elephant-grass genotypes. It was applied a randomized block experimental design with two replications. The experimental unit consisted of one 5.5 m-line with spacing of 2 m, totaling 11 m2. The plot area was a sampling at the center of the plot. Morpho-agronomic, multi-categorical, and phenological traits were assessed. The estimation of the genetic distance matrix was carried out by means of the joint analysis of the quantitative and qualitative variables obtained based on the Gower algorithm. The data were analyzed using GENES and R program. The results revealed that there is a wide genetic variability among the accessions studied. Some accessions show low genetic distances, which indicates that they are duplicates in the germplasm bank.

Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus avium L.)

Identification of genetic polymorphisms and subsequent development of molecular markers is important for marker assisted breeding of superior cultivars of economically important species. Sweet cherry (Prunus avium L.) is an economically important non-climacteric tree fruit crop in the Rosaceae family and has undergone a genetic bottleneck due to breeding, resulting in limited genetic diversity in the germplasm that is utilized for breeding new cultivars. Therefore, it is critical to recognize the best platforms for identifying genome-wide polymorphisms that can help identify, and consequently preserve, the diversity in a genetically constrained species. For the identification of polymorphisms in five closely related genotypes of sweet cherry, a gel-based approach (TRAP), reduced representation sequencing (TRAPseq), a 6k cherry SNParray, and whole genome sequencing (WGS) approaches were evaluated in the identification of genome-wide polymorphisms in sweet cherry cultivars. All platforms facilitated detection of polymorphisms among the genotypes with variable efficiency. In assessing multiple SNP detection platforms, this study has demonstrated that a combination of appropriate approaches is necessary for efficient polymorphism identification, especially between closely related cultivars of a species. The information generated in this study provides a valuable resource for future genetic and genomic studies in sweet cherry, and the insights gained from the evaluation of multiple approaches can be utilized for other closely related species with limited genetic diversity in the breeding germplasm.

Diversity and genetic stability in banana genotypes in a breeding program using inter simple sequence repeats (ISSR) markers.

Banana (Musa spp) is a fruit species frequently cultivated and consumed worldwide. Molecular markers are important for estimating genetic diversity in germplasm and between genotypes in breeding programs. The objective of this study was to analyze the genetic diversity of 21 banana genotypes (FHIA 23, PA42-44, Maçã, Pacovan Ken, Bucaneiro, YB42-47, Grand Naine, Tropical, FHIA 18, PA94-01, YB42-17, Enxerto, Japira, Pacovã, Prata-Anã, Maravilha, PV79-34, Caipira, Princesa, Garantida, and Thap Maeo), by using inter-simple sequence repeat (ISSR) markers. Material was generated from the banana breeding program of Embrapa Cassava & Fruits and evaluated at Embrapa Coastal Tablelands. The 12 primers used in this study generated 97.5% polymorphism. Four clusters were identified among the different genotypes studied, and the sum of the first two principal components was 48.91%. From the Unweighted Pair Group Method using Arithmetic averages (UPGMA) dendrogram, it was possible to identify two main clusters and subclusters. Two genotypes (Garantida and Thap Maeo) remained isolated from the others, both in the UPGMA clustering and in the principal cordinate analysis (PCoA). Using ISSR markers, we could analyze the genetic diversity of the studied material and state that these markers were efficient at detecting sufficient polymorphism to estimate the genetic variability in banana genotypes.

Molecular diversity and population structure of the Ethiopian lentil (Lens Culinaris 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.

A comparative assessment of ISSR, RAPD, IRAP, & REMAP molecular markers in Zingiber officinale germplasm characterization

One hundred and ninety four collection of ginger germplasm were genetically evaluated using four PCR based markers employing 7 ISSR, 9 rice-SSR, 6 IRAP pairs and 25 combinations of REMAP primers. Each marker technique could discriminate the accessions with varied efficiency of polymorphism (83.6–88.2%). The resolving power and marker index were estimated to be maximum in REMAP (5.24 & 4.18) and minimum in IRAP (3.92 & 3.25) techniques. The combined data matrices of RAPD-ISSR and retrotransposon displayed similar polymorphism 87.03% and 87.5%, respectively. All the four techniques broadly classified the germplasm into two major clusters. Correlations between combined similarity matrices of the two techniques to the individual matrices were high (0.90–0.97). Comparison of the techniques helped in generating a common index, reflecting the degree of DNA polymorphism generated in each case. The study demonstrated REMAP and RAPD, employing rice-SSR markers, are the markers of choice in ginger germplasm genetic diversity assessment. The information will help in crop selection, efficient management and conservation of ginger genetic resources.

PHENOTYPIC DIVERGENCE AMONG GRAPEVINE ACCESSIONS OF THE GERMPLASM COLLECTION AT IAC

Germplasm bank characterization as well as adequate statistical methods allows the identification of divergent parents. Therefore, this study aimed to evaluate the genetic divergence among 56 accessions of grapevine of the Germplasm Collection at Instituto Agronomico - IAC, characterized by eight quantitative traits. Multivariate analyses were used to quantify the divergence among the accessions. Euclidian distance, principal components and Tocher?s clustering method were applied. The Tocher?s method applied to the matrix of Euclidian distance with scores of principal components discriminated seven groups, with the first two comprised 69.64% and 17.86% respectively of total access. About 77,27% of the total variation was explained by the first two main components and 86,94% was explained by the three first main components obtained with eight components analysis. Thus, the multivariate analysis to study genetic diversity applied to the quantitative characters (Tocher?s clustering method and principal components) agreed among themselves, being efficient for analysis of the genetic diversity of germplasm of grapevine at IAC, which can be used for guidance in future crosses for breeding of this species. However, additional characteristics related to productivity, cycle and quality of most will be realized and added to these works of diversity.

Germplasm genetic diversity of Myrica rubra in Zhejiang Province studied using inter-primer binding site and start codon-targeted polymorphism markers

The genetic diversity of 31 germplasm resources of Myrica rubra from Zhejiang Province, the major gathering site and the largest producer of M. rubra in China, was investigated using inter-primer binding site (iPBS) and start codon-targeted polymorphism (SCoT) markers. Cluster analysis was performed using unweighted pair-group method arithmetic averages. The results showed that the genetic similarity (GS) values of the samples tested using the two molecular markers were within the range of 0.5 to 0.94. Approximately 452 distinct bands, including 401 polymorphic bands, were obtained using 38 pairs of primers, and the polymorphism rate was 88.72%. A threshold GS value of 0.70 was used to divide the 31 M. rubra samples into three groups. The four major M. rubra varieties in China that originated from Zhejiang Province (Dongkui, Biqi, Dingaomei, and Zhoushanwandaomei) showed significant genetic differences. Dongkui was more distantly related to Dingaomei and Zhoushanwandaomei compared to Biqi. The GS values of the Dongkui mutant samples DB1 and DB2 were 0.77 and 0.80, respectively, and thus they were considered to be more closely related. The GS values of Biqi and its bud mutants Zaoqi, Yongxuan 56, and Wuzi were 0.66, 0.59, 0.658, and 0.65, respectively, with Zaoqi showing more differences than the other three varieties. Zhoushanwandaomei and Shangyubaiyangmei, Heijing and Wuzi, Yongjiacimei and Yuanqiaoshuimei, Dongaowumei and Jiangkou Dongkui monoecious plants, Tuda and Liuyemei, Xuemei and Haochimei, Donglingwubian and Muyemei, DB2 and Dongkuimushu, and Dongkui and Shanzhan Dongkui monoecious plants were all clustered within the same subgroup, indicating that these were more closely related. The GS of both Xiyegaozhuang and Jiazhaizao was 0.94, suggesting that these varieties were synonymous. The GS of Linhaiyangpingmei was 0.55, indicating that it had the most distant genetic relationship. For the three major resource-gathering sites – Taizhou, Ningbo, and Wenzhou – the intra-regional genetic germplasm base was narrow with relatively extensive exchanges, and the sites were extra-regionally independent. Our study results are consistent with those of morphological index analysis, have identified the conditions in which the genetic diversity of M. rubra germplasm in Zhejiang Province occurs, and have established a foundation for genetic breeding and germplasm research and identification.

Mining of microsatellite markers using next generation sequencing data and its application in genetic relationship analysis of tartary buckwheat (Fagopyrum tataricumGaertn)

Fagopyrum genus is composed of about 20 species and among them two major species, common buckwheat (F. esculentum) and tartary buckwheat (F. tataricum). SSR markers are only reported in common buckwheat with lower numbers based on enriched repeat libraries and next-generation sequencing (NGS) is a cost-effective alternative. Here we report the development of new cDNA SSR (cSSR) markers characterized from transcriptome sequence data of F. esculentum and F. tataricum using NGS and these cSSR markers were applied for the validation of buckwheat germplasm. From the transcriptome sequences, a total of 8,360 and 6,518 putative cSSR markers were identified in common and tartary buckwheat, respectively, using SSR Locator. Among the cSSR markers, tetra-mer repeats are most abundant and occurred in rates of 54.9 and 37.3% in common and tartary buckwheat, respectively. To test the usefulness of newly developed cSSR markers with previously developed SSR markers based on the SSR motif enrichment library, in analysis of genetic relationship in tartary buckwheat, we selected five representative cSSR markers and applied to investigate the polymorphism of tartary buckwheat germplasm and found these markers can be applied in genetic diversity of germplasm with high polymorphism.

Marker-assisted Backcrossing for Identification of Salt Tolerant Rice Lines

SSR or microsatellite markers are proved to be ideal for making genetic maps, assisting selection and studying genetic diversity in germplasm. SSR markers are playing important role to identify gene for salt tolerance that can be helpful for plant breeders to develop new cultivars. The experiment was conducted during the period from July 2009 to November 2010 in the experimental field and Biotechnology Laboratory of Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh to identify salt tolerant rice line of BC1F1 progenies of Binadhan-5 x FL-478 using SSR markers. Salt tolerant genotype, FL-478 was crossed with high yielding variety, Binadhan-5. Randomly selected 40 BC1F1 progenies along with their two parents (Binadhan-5, FL-478 and F1) were genotyped with microsatellite or SSR markers for identification of salt tolerant rice lines. Parental polymorphism survey was assayed by 10 SSR markers and three polymorphic SSR markers viz., RM 336, RM 510, and RM 585 were selected to evaluate BC1F1 rice lines for salt tolerance. In respect of Primer RM 336, 11 lines were found as salt tolerant and 25 lines were heterozygous and 3 lines were susceptible. Primer RM 510 identified two tolerant, 14 heterozygous and 22 susceptible lines. And primer RM 585 identified 4 lines as tolerant and 35 lines as susceptible. Thus, these markers could be efficiently used in tagging salt tolerant genes, in marker-assisted selection and quantitative trait loci (QTL) mapping. The selected BC1F1 could be used for developing BC2F1 and BC2F2 and mapping genes for salinity tolerance. DOI: http://dx.doi.org/10.3329/ijarit.v2i2.14008 Int. J. Agril. Res. Innov. & Tech. 2 (2): 1-8, December, 2012

Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

Genome-wide distribution of genetic diversity and linkage disequilibrium in elite sugar beet germplasm

BackgroundCharacterization of population structure and genetic diversity of germplasm is essential for the efficient organization and utilization of breeding material. The objectives of this study were to (i) explore the patterns of population structure in the pollen parent heterotic pool using different methods, (ii) investigate the genome-wide distribution of genetic diversity, and (iii) assess the extent and genome-wide distribution of linkage disequilibrium (LD) in elite sugar beet germplasm.ResultsA total of 264 and 238 inbred lines from the yield type and sugar type inbreds of the pollen parent heterotic gene pools, respectively, which had been genotyped with 328 SNP markers, were used in this study. Two distinct subgroups were detected based on different statistical methods within the elite sugar beet germplasm set, which was in accordance with its breeding history. MCLUST based on principal components, principal coordinates, or lapvectors had high correspondence with the germplasm type information as well as the assignment by STRUCTURE, which indicated that these methods might be alternatives to STRUCTURE for population structure analysis. Gene diversity and modified Roger's distance between the examined germplasm types varied considerably across the genome, which might be due to artificial selection. This observation indicates that population genetic approaches could be used to identify candidate genes for the traits under selection. Due to the fact that r2 >0.8 is required to detect marker-phenotype association explaining less than 1% of the phenotypic variance, our observation of a low proportion of SNP loci pairs showing such levels of LD suggests that the number of markers has to be dramatically increased for powerful genome-wide association mapping.ConclusionsWe provided a genome-wide distribution map of genetic diversity and linkage disequilibrium for the elite sugar beet germplasm, which is useful for the application of genome-wide association mapping in sugar beet as well as the efficient organization of germplasm.

Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes

Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.