Mean Gene Diversity Research Articles

The Genetic Diversity and Population Structure of Different Geographical Populations of Bottle Gourd (Lagenaria siceraria) Accessions Based on Genotyping-by-Sequencing

Lagenaria siceraria (Molina) Standl is an important horticultural and medicinal crop grown worldwide in the food and pharmaceutical industries. The crop exhibits extensive phenotypic and genetic variation useful for cultivar development targeting economic traits; however, limited genomic resources are available for effective germplasm characterization into breeding and conservation strategies. This study determined the genetic relationships and population structure in a collection of different accessions of bottle gourd derived from Chile, Asia, and South Africa by using single-nucleotide polymorphism (SNP) markers and mining of simple sequence repeat (SSR) loci derived from genotyping-by-sequencing (GBS) data. The GBS resulted in 12,766 SNPs classified as moderate to highly informative, with a mean polymorphic information content of 0.29. The mean gene diversity of 0.16 indicated a low genetic differentiation of the accessions. Analysis of molecular variance revealed less differentiation between (36%) as compared to within (48%) bottle gourd accessions, suggesting that a random mating system dominates inbreeding. Population structure revealed two genetically differentiated groups comprising South African accessions and an admixed group with accessions of Asian and Chilean origin. The results of SSR loci mining from GBS data should be developed and validated before being used in diverse bottle gourd accessions. The SNPs markers developed in the present study are useful genomic resources in bottle gourd breeding programs for assessing the extent of genetic diversity for effective parental selection and breeding.

Genome-Wide Assessment of Population Structure and Genetic Diversity of the Global Finger Millet Germplasm Panel Conserved at the ICRISAT Genebank.

Finger millet [Eleusine coracana (L.) Gaertn.] is an important climate-resilient nutrient-dense crop grown as a staple food grain in Asia and Africa. Utilizing the full potential of the crop mainly depends on an in-depth exploration of the vast diversity in its germplasm. In this study, the global finger millet germplasm diversity panel of 314 accessions was genotyped, using the DArTseq approach to assess genetic diversity and population structure. We obtained 33,884 high-quality single nucleotide polymorphism (SNP) markers on 306 accessions after filtering. Finger millet germplasm showed considerable genetic diversity, and the mean polymorphic information content, gene diversity, and Shannon Index were 0.110, 0.114, and 0.194, respectively. The average genetic distance of the entire set was 0.301 (range 0.040 – 0.450). The accessions of the race elongata (0.326) showed the highest average genetic distance, and the least was in the race plana (0.275); and higher genetic divergence was observed between elongata and vulgaris (0.320), while the least was between compacta and plana (0.281). An average, landrace accessions had higher gene diversity (0.144) and genetic distance (0.299) than the breeding lines (0.117 and 0.267, respectively). A similar average gene diversity was observed in the accessions of Asia (0.132) and Africa (0.129), but Asia had slightly higher genetic distance (0.286) than African accessions (0.276), and the distance between these two regions was 0.327. This was also confirmed by a model-based STRUCTURE analysis, genetic distance-based clustering, and principal coordinate analysis, which revealed two major populations representing Asia and Africa. Analysis of molecular variance suggests that the significant population differentiation was mainly due to within individuals between regions or between populations while races had a negligible impact on population structure. Finger millet diversity is structured based on a geographical region of origin, while the racial structure made negligible contribution to population structure. The information generated from this study can provide greater insights into the population structure and genetic diversity within and among regions and races, and an understanding of genomic-assisted finger millet improvement.

Exploring the genetic diversity and population structure of scarlet eggplant germplasm from Rwanda through iPBS-retrotransposon markers.

Scarlet eggplant (Solanum aethiopicum gr. gilo) is a part of African indigenous vegetables and acknowledged as a source of variations in the breeding of Brinjal. Since its genetic diversity is still largely unexplored, therefore genetic diversity and population structure of this plant were investigated in this study. Scarlet eggplant germplasm made of fifty-two accessions originated from two districts of Rwanda was assessed by employing the iPBS-retrotransposon markers system. Twelve most polymorphic primers were employed for molecular characterization and they yielded 329 total bands whereupon 85.03% were polymorphic. The recorded mean polymorphism information content was 0.363 and other diversity indices such as; mean the effective number of alleles, mean Shannon's information index and gene diversity with the following values; 1.298, 0.300 and 0.187 respectively. A superior level of diversity was noticed among accessions from Musanze district. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) gathered scarlet germplasm in a divergence manner to their collection district. Analysis of molecular variance (AMOVA) displayed that the utmost variations (81%) in scarlet eggplant germplasm are resulting in differences within populations. The extensive diversity of scarlet eggplant in Rwanda might be used to form the base and genetic resource of an exhaustive breeding program of this economically important African indigenous vegetable. For instance, accessions MZE53 and GKE11 might be proposed as parent candidates due to their high relative genetic distance (0.6781).

Genetic diversity of common bean (Phaseolus vulgaris L.) germplasm from Serbia, as revealed by single sequence repeats (SSR)

Genetic diversity and structure of common bean (Phaseolus vulgaris L.) germplasm from Serbia, comprising 118 landraces and 18 cultivars, was assessed with the application of 27 Single Sequence Repeats (SSR) markers. Thirteen accessions from Agricultural Institute of Slovenia were used as references for gene pool determination. Main parameters of genetic diversity were calculated for each SSR loci, i.e. number of different and rare alleles, number of effective alleles, Shannon's information index, observed and expected heterozygosity and polymorphic information content. A total of 445 allelic variants, with 16.5 alleles per locus on average, were detected. Mean gene diversity (He = 0.79) indicated sufficient reservoir of genetic variation preserved in studied bean germplasm. Landraces displayed higher variability compared to cultivars (405 in relation to 233 allelic variants). Genetic structure and relatedness of accessions was assessed by model-based method and hierarchical clustering method in combination with genetic distance calculation. The Bayesian clustering model implemented in STRUCTURE software, on the primary level (K = 2), revealed clear separation of accessions into two groups, corresponding to gene pool affiliation. Mesoamerican gene pool (M) was represented with 23.5% of accessions, while Andean (A) was larger, composed of 68.4% of studied germplasm. Small group (8.1%) showed admixed genetic structure between two gene pools. Additional variation in respect to two recognized gene pools was revealed (K = 3), whose basis was acknowledged to be within Andean gene pool. Further subdivision of accessions (K = 8), mainly according to the seed forms, was observed. Genetic distance analysis associated with Neighbour-joining clustering method revealed grouping pattern of landraces and cultivars corresponding to the gene pool and their seed phenotypes. Classification and structuring of the bean accessions according to and beyond the gene pool of origin should facilitate conservation strategies and breeding of this material. Combining the information of phenotypic variation obtained in previous research and molecular data reveled in this study will assist in selection of parental components for breeding, or in the choice of smaller sample in order to further acknowledge their breeding value. In addition, obtained results of this work should serve as an additional information on common bean germplasm variation in Western Balkans and beyond, in Europe.

High Genetic Diversity in Flavobacterium psychrophilum Isolates from Healthy Rainbow Trout (Oncorhynchus mykiss) Farmed in the Same Watershed, Revealed by Two Typing Methods.

Flavobacterium psychrophilum affects salmonid health worldwide and causes economic losses. The genetic diversity of the pathogen must be considered to develop control methods. However, previous studies have reported both high and low levels of genetic diversity. The present longitudinal study aimed at assessing the genetic diversity of F. psychrophilum at a small temporal and geographic scale. Four farms located on the same watershed in France were studied. Rainbow trout (Oncorhynchus mykiss) batches were monitored, and apparently healthy individuals were sampled over 1 year. A total of 288 isolates were recovered from fish organs (gills and spleen) and eggs. Pulsed field gel electrophoresis revealed high genetic diversity. Multilocus sequence typing performed on a selection of 31 isolates provided congruent results, as follows: 18 sequence types (STs) were found, of which 13 were novel. The mean gene diversity (H = 0.8413) was much higher than that previously reported for this host species, although the sampling was restricted to a single watershed and 1 year. Seven isolates out of 31 were assigned to clonal complex ST10 (CC-ST10), which is the predominant clonal complex in the main salmonid production areas. A split decomposition tree reflected a panmictic population. This finding is important for aquaculture veterinarians in their diagnostic procedure, as the choice of adequate antibiotic treatment is conditioned by the correct identification of the causative agent. Furthermore, this study expands our knowledge on genetic diversity required for the development of an effective vaccine against F. psychrophilumIMPORTANCE The bacterium Flavobacterium psychrophilum is a serious pathogen in many fish species, especially salmonids, that is responsible for considerable economic losses worldwide. In order to treat infections and to develop vaccines, the genetic diversity of this bacterium needs to be known. We assessed the genetic diversity of F. psychrophilum isolates from apparently healthy rainbow trout raised in several fish farms in the same watershed in France. Two different genotyping methods revealed high diversity. The majority of isolates were unrelated to clonal complex sequence type 10 (CC-ST10), the clonal complex that is predominant worldwide and associated with disease in rainbow trout. In addition, we found 13 novel sequence types. These results suggest that a diverse subpopulation of F. psychrophilum may be harbored by rainbow trout.

Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers.

Knowledge of genetic diversity in plant germplasm and the relationship between genetic factors and phenotypic expression is vital for crop improvement. This study's objectives were to understand the extent of genetic diversity and population structure in 60 common bean genotypes from East and Southern Africa. The common bean genotypes exhibited significant (p<0.05) levels of variability for traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield per hectare in kilograms (GYD). About 47.82 per cent of the variation among the genotypes was explained by seven principal components (PC) associated with the following agronomic traits: NPP, NFF (nodes to first flower), DTF, GH (growth habit) and GYD. The SNP markers revealed mean gene diversity and polymorphic information content values of 0.38 and 0.25, respectively, which suggested the presence of considerable genetic variation among the assessed genotypes. Analysis of molecular variance showed that 51% of the genetic variation were between the gene pools, while 49% of the variation were within the gene pools. The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.

Evaluation of dark jute SSR markers and morphological traits in genetic diversity assessment of jute mallow (Corchorus olitorius L.) cultivars

The jute mallow (C. olitorius L.) is an important nutritious green leafy vegetable in the tropical region of Africa. This study assesses the extent of genetic diversity and intra-specific relationships among 16 cultivated jute mallows of Nigeria (14), [Ghana (1) and Togo (1), used as checks, evaluating 16 dark jute SSR markers and 16 morphological traits (quantitative and qualitative). The study reveals moderate to high variation among the cultivars in the number of pods, pod yield and plant height traits. Based on the principal component (PC) analysis of the quantitative traits, the pod length, pod width, number of pods, pod yield and plant height are important traits composing PC1. On the other hand, the pod pedicel length and days of 50% flowering traits are highly correlated variables in PC2. Pod length, pod width, pod pedicel length and plant height account for the total diversity. Two main groups (I and II) and an outgroup are identified among the 16 cultivars based on the quantitative traits. among the cultivars, leaf shapes identified are ovate (38% of cultivars), lanceolate (6%), oblanceolate (25%) and palmately lobed (31%). Three markers which have monomorphic alleles are excluded and thirteen markers are used to analyse the genetic diversity. A total of 41 alleles are amplified using the 13 polymorphic markers with an average of 2.75 per locus. The mean polymorphism information content (PIC) value is 0.42, ranging from 0.06 to 0.73. The mean gene diversity or expected heterozygosity = 0.05 (from 0.06 to 0.76). The observed heterozygosity (Ho) ranges from 0.00 to 0.88, with a mean of 0.60. The mean genetic dissimilarity is 0.35. Thus, the SSR data indicate a moderate genetic dissimilarity within jute mallow under study. Clustering using the neighbour-joining dendrogram predicated on the SSR data separates the cultivars into three major groups in which the two cultivars from Ghana and Togo show distinctiveness from the cultivars from Nigeria. Principal coordinate analysis of SSR data is consistent with neighbour-joining groupings. The study based on a set of dark jute markers and morphological traits reveals that the extent of genetic diversity of cultivated jute mallow and could be used in germplasm evaluation. In addition to the knowledge of the high genetic variability observed in the number of pod and the yield of some of the studied cultivars, further efforts are needed to characterise the cultivar pods’ nutritive values for human health.

Genetic diversity of selected pigmented traditional rice (Oryza sativa L.) varieties from Mindanao, Philippines using agromorphological traits and simple sequence repeats markers

Philippine pigmented traditional rice varieties (TRVs) offer potential novel genes for genetic improvement. In this study, forty-three pigmented traditional rice varieties (TRVs) from Region X, XII and XIII in Mindanao were evaluated using 47 agromorphological (22 qualitative and 25 quantitative) traits, grain chemical properties, disease reaction, insect pests, and 64 SSR markers. The standardized Shannon–Weaver diversity index for phenotypic diversity averaged at 0.30 for qualitative and 0.88 for quantitative traits. Desirable traits observed in the TRVs include erect flag leaf, pubescent leaf blade, and strong culm for lodging resistance. Three TRVs, Malagkit (CollNo. 4555), Dinorado (CollNo. 11071), and Canayo (CollNo. 12794) showed resistance to blast. While Kabuyok (CollNo. 1091), Kabuyog (CollNo. 11052), Dinorado (CollNo. 12786), Lubang (Red) (CollNo. 4541), Manganahaw (CollNo. 4570), Palawenyo (CollNo. 6361), Boringan (CollNo. 4291), Mixture from Kabuyok (CollNo. 11070) and Mimis (CollNo. 1092) recorded intermediate resistance to whiteheads. Tapul (CollNo. 5156) was identified to have blast resistance with desirable grain chemical properties: intermediate amylose content, low gelatinization temperature and medium cooked rice. The PIC values revealed that RM26550, RM28166, RM10665, RM27492 and RM23251 could be the best markers for genetic diversity estimation of these TRVs. The diversity at gene level showed average of 3.48 alleles ranging from 2 to 11 per locus. Mean gene diversity (H) value for all SSR loci was at 0.34, indicates moderate genetic diversity of TRVs used in the study. These pigmented TRVs can be tapped for pests/diseases resistance, and grain quality research, direct utilization or as parents in specific breeding purposes.

DNA fingerprinting and genetic diversity analysis of world quinoa germplasm using iPBS-retrotransposon marker system

Quinoa is an important staple food crop for millions of impoverished rural inhabitants of the Andean region. Quinoa is considered a good source of protein,vitamins, minerals, and antioxidants. This study aimed to investigate the genetic diversity and population structure of world quinoa germplasm originating from 8 countries through the iPBS-retrotransposon marker system. Molecular characterization was performed using the 11 most polymorphic primers. A total of 235 bands were recorded, of which 66.8% were polymorphic. Mean polymorphism information content (PIC) was 0.410. Various diversity indices including mean effective number of alleles (1.269), mean Shannon's information index (0.160) and gene diversity (0.247) revealed the existence of sufficient amount of genetic diversity in studied germplasm. Bolivia-17 and Mexico-1 were found to be genetically distinct accessions and can be suggested as candidate parents for future breeding activities. Various diversity indices were also calculated among germplasm collection counries and the results clearly showed the existence of higher genetic diversity in Bolivian and Peruvian accessions. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) grouped quinoa germplasm according to their collection country. Analysis of molecular variance (AMOVA) revealed that most of the variations (69%) in world quinoa germplasm are due to differences within populations. Findings of this study can be used for deeper understanding of the genetic relationship and in the determination of appropriate breeding and conservation strategies for quinoa.

Revealing the genetic diversity of maize (Zea mays L.) populations by phenotypic traits and DArTseq markers for variable resistance to fall armyworm

The fall armyworm (FAW) is a gregarious insect pest causing substantial yield losses and crop failures in maize and related cereal crops in sub-Saharan Africa due to a lack of resistant varieties and integrated control options. Genetic variation for economic traits including resistance to the FAW damage is a prerequisite in maize improvement programs. The objective of this study was to determine the genetic diversity of 59 maize genotypes of diverse genetic background with variable resistance to fall armyworm, using phenotypic traits and SNP-based DArT markers. The test genotypes were profiled using agro-morphological traits, FAW damage parameters, and Diversity Array Technology Sequencing-derived single nucleotide polymorphism (SNP) markers. Significant (p < 0.001) differences were observed among the genotypes for 13 phenotypic traits with phenotypic coefficient of variation ranging from 2.19 to 51.79%. Notable phenotypic variation was observed for ear position, grain yield, FAW induced leaf and cob damage. The mean gene diversity and polymorphic information content were 0.29 and 0.23, respectively, reflecting a moderate level of genetic variation among the test genotypes when assessed using SNP markers. Analysis of the molecular variance revealed greater genetic variance within a population rather than between populations. Population structure and cluster analysis grouped the test populations into two main clusters. The following genetically divergent open pollinated varieties were selected with favourable agronomic performance and FAW resistance for population improvement or hybrid breeding: Pool 16, ZM 4236 and ZM 7114. The genetic diversity detected within and among the tested populations will facilitate the breeding of maize varieties incorporating farmer-preferred agronomic traits and FAW resistance in Zambia and related agro-ecologies.

Genetic diversity analysis of common bean (Phaseolus vulgaris L.) genotypes for resistance to Mexican bean weevil (Zabrotes subfasciatus), using single nucleotide polymorphism and phenotypic markers

ABSTRACT The objective of this study was to examine the genetic diversity present among 297 common bean genotypes using 2554 SNPs and 12 insects and seed-related traits. The phenotyping was done under laboratory condition while the genotyping was conducted by using the Illumina SNP BeadChip. High phenotypic diversity among traits were recorded, ranging from 0.87 to 0.96, with a mean of 0.92. Principal component and discriminant analyses identified four PCs and three discriminant functions, which explained 82% and 100% of the total phenotypic variations among genotypes, respectively. Polymorphic Information Content ranged from 0.21 to 0.38, with a mean of 0.34. The mean gene diversity among genotypes ranged from 0.24 to 0.50, with a mean of 0.44. Genetic distance ranged from 0.19 to 0.82, with a mean of 0.62, while the phenotypic distance ranged from 0.00 to 1.00, with a mean of 0.64 were observed aamong genotypes. The analysis of molecular variance revealed highly significant differences (p<0.001) among and within individuals and among populations. Both the SNP and the phenotypic markers grouped the 297 genotypes into two major distinct clusters and three sub-clusters. This information is useful for identification and development of common bean germplasm with economically valuable traits and the conservation and utilization of genotypes.

Transcriptome profiling, simple sequence repeat markers development and genetic diversity analysis of potential industrial crops Capsicum chinense and C. frutescens of Northeast India

Capsaicinoids, a group of secondary metabolites (alkaloids) which imparts hot property, are unique to the Capsicum fruits and have high value in the pharmaceutical and food industries. In spite of having high capsaicinoids content with ethnopharmacological and economic importance, the C. chinense and C. frutescens of the Northeast India, are underexplored for the genetics and breeding programs. In this study, we developed transcriptome-based Simple sequence repeat (SSR) markers and analyzed the expression(s) of capsaicinoids and carotenoid biosynthesis pathway genes in flower and fruit tissues at three developmental stages (early, breaker and mature) of C. chinense, C. frutescens and C. annuum. A total of 4988 and 4781 genic SSRs were identified from 123,118 and 121,017 de novo assembled unigenes, in C. chinense and C. frutescens, respectively. Also, the reference-based transcriptome analysis identified 70.8–73.6 % commonly expressed transcripts in all tissues besides 2929, 1327, 1193 and 937 unique transcripts in flower, early, breaker and mature fruits, respectively. The gene expression profiling showed significantly high expression of the key capsaicinoids and carotenoid biosynthetic pathway genes at breaker and mature fruit stages. Furthermore, in silico analysis identified a total of 335 polymorphic SSRs between C. chinense and C. frutescens with allelic size difference of >4 bases. The trinucleotide repeats was found to be predominant in both C. chinense (50.6 %) and C. frutescens (52.2 %). High genetic-diversity of SSRs was observed with mean gene diversity of 0.51 and polymorphism information content (PIC) of 0.53. Based on twenty polymorphic SSRs, the UPGMA cluster analysis differentiated 96 genotypes belonging to C. chinense, C. frutescens and C. annuum into distinct groups. The identified SSRs and diverse Capsicum genotypes will serve as important genetic resources for future applications in genetics study and breeding of Capsicum varieties with improved metabolites (pungency, carotenoids etc.) and agronomic traits (fruit shape, size etc.) for agricultural, food and pharmaceutical industries.

Genetic differentiation of selected drought and heat tolerant wheat genotypes using simple sequence repeat markers and agronomic traits

Development of wheat (Triticum aestivum L.) varieties with increased yield potentials that are adapted to drought and heat stresses requires genetically differentiated and complementary parents. The present study established genetic profiles of heat and drought tolerant wheat genotypes through SSR loci and agronomic traits for breeding. Fourteen candidate wheat genotypes selected from the International Maize and Wheat Improvement Centre (CIMMYT) and a local variety were genotyped using 10 diagnostic SSR markers. Further, the genotypes were evaluated for agronomic performance under non-stressed (NS) and drought-stressed (DS) conditions. The mean gene diversity of 0.75 confirmed genetic diversity of evaluated wheat genotypes. Analysis of molecular variance accounted for 75 and 25% of the variation within and among genotypes respectively. Significant differences were observed for assessed agronomic traits under NS and DS conditions. There were significant (p < 0.01) correlations between grain yield and plant height (r = -0.42) and spike length (r = 0.39) under DS conditions. Cluster analysis allocated test genotypes to three genetic groups and aided selection of genetically unrelated and high-yielding heat and drought tolerant genotypes such as SM04, SM19 and SM32. These are useful germplasm for developing breeding populations for improved yield gains.

Genetic Diversity and Structure of Tunisian Local Pear Germplasm as Revealed by SSR Markers

Growing pear has a long tradition in Tunisia, and numerous local cultivars possessing an excellent adaptability and resilience potential to climatic variation are present. This large adaptability is associated with an important genetic diversity, which is threatened to erosion. Appropriate measures have to be taken in order to properly evaluate and conserve this local material. Microsatellite markers were used to assess the level of genetic diversity among Tunisian pear germplasm, and compare it with some European varieties and wild pear species. 61 pear accessions representing eight groups (six groups from Tunisia, one from Northern Europe and another group composed of wild pear) have been genotyped using SSR markers derived from apple and pear. The pear accessions showed a significant polymorphism and 95 polymorphic alleles were found. The number of alleles per locus varied from 5 for CH04e03 locus to 14 for CH01d09 locus with an average of 9.4 alleles per locus. Moreover, the mean gene diversity (He) per locus ranged from 0.192 to 0.752. Genetic distance values and cluster analyses revealed high genetic similarities among the Tunisian groups. Factorial correspondence analysis (FCA) categorized the accessions into three independent groups where Tunisian local accessions agglomerated together distantly from European and wild pear accessions. Additionally, UPGMA dendrogram grouped accessions into two clusters, confirmed thereafter by the Bayesian model-based Structure analysis. The results showed 16 putative triploid accessions found in the local germplasm. This study provides valuable information to develop strategies of local pear conservation and use.

Development and characterization of novel microsatellite markers in Puccinia striiformis f.sp. tritici and their transferability in Puccinia species

AbstractPuccinia striiformis f.sp. tritici (Pst) and P. striiformis f.sp. hordei (Psh) causing stripe rust disease in wheat and barley, respectively, are two devastating phytopathogens. Microsatellite/simple sequence repeat (SSR) markers are increasingly being utilized for analysis of genetic diversity, diagnosis, population structure and possible migratory routes of plant pathogens. In the current study, novel polymorphic SSR markers were designed for Pst using the genomic sequences of PST‐78 isolate. A total of 1,191 SSR motifs, comprising 30% each of di‐ and tri‐nucleotide type of repeats, 17% of penta‐nucleotide, 15% of tetra‐nucleotide and 8% of hexa‐nucleotide repeats, were detected through in silico scanning of PST‐78 genomic sequences. Polymorphism was detected by nine of the 50 designed SSRs (PsSSRs) in seven stripe rust pathotypes of wheat and barley. The mean number of alleles per SSR locus, mean polymorphism information content (PIC), mean heterozygosity, mean major allele frequency (MAF) and mean gene diversity were 2.33, 0.34, 0.33, 0.71 and 0.40, respectively. The dendrogram analysis suggested that newly developed PsSSR markers could distinguish stripe rust pathotypes based on their virulence phenotype. Further, the cross‐genera and cross‐species amplification test of these markers in 14 different rust pathotypes revealed that 9 PsSSRs are capable of amplification in Pst species infecting wild grass, followed by 6 PsSSRs in Pt, 3 PsSSRs in Pgt, 1 PsSSRs in Puccinia species on barberry and Melampsora lini. Thus, the transferability of PsSSRs to other species reduced with increasing genetic distance of target species. These newly designed SSR markers expand the available Pst SSR marker resources and allow better genetic studies.

Identification of New Sources of Rust Resistance in Cowpea (Vigna Unguiculata L. Walp) Germplasm Using Simple Sequence Repeat Markers

The demand for resistance cowpea to rust infection has currently increased due to considerable yield losses caused by the fungal pathogen. The study assessed available cowpea genotypes for rust resistance using simple sequence repeat (SSR) markers. Out of 100 cowpea genotypes screened, 97% showed presence of the markers whilst 3% showed absence of the markers. Among the cowpea were 72% resistance, 16% moderate resistance and 9% low resistance to rust. The markers revealed mean high allele frequency (0.86) and low gene diversity (0.24) and polymorphism information content (0.21) among the cowpea genotypes. The markers co-inherited with mean regression value greater than 0.1. There was no clear pattern of clustering among the cowpea genotypes. The cowpea genotypes with rust resistance traits could serve as good sources of germplasm for cultivation or resilient genes with rust target in breeding programmes to improve the crop.

Genetic Divergence and Heritability Study of Some NERICA Mutant Lines and Their Parents Using Microsatellites Marker and Morphological Traits in Rice

New Rice of Africa (NERICA) is drought tolerant and early maturing inter specific rice variety which was introduced in Bangladesh from Uganda in 2009. But the field record of NERICA was not very promising. In order to develop NERICA varieties suitable for agro-climatic conditions of Bangladesh different variations in yield contributing characters are required.In the experiment, physical mutagen treated (250, 300 and 350 Gy Gamma-rays) 18 NERICA mutant lines were selected from M4 to M5 generations along with 3 parents (NERICA-1, NERICA-4, NERICA-10) for morphological and molecular evaluation in orderto identify desired mutant linesusing 12 yield attributing characters and 3 simple sequence repeat (SSR) markers. We also estimated heritability, genetic advance and correlation among the studied morphological traits to identify besttraits based on which further selection could be made. Pearson’s correlation co-efficient of 12 morphological traits indicated that yield per plant had significant positive correlation with the number of tiller, number of effective tiller, panicle length, number of filled grainsper panicle and 1000 grain weight but negative correlation with Plant height and days to maturity. Broad sense heritability ( ) ranged from 71% to 99% while genetic advances in percent mean (GA%) varied from 10% to 60%. Yield per plant, unfilled grains per panicle, number of total tiller, number of effective tiller showed high heritability along with genetic advance as percent of the mean (GA%) value. A total of 24 alleles were detected by 3 SSR markers. The mean gene diversity and Polymorphism Information Content (PIC) values was 0.821 and 0.797, respectively. Dendrogram constructed based on SSR markers clustered the genotypes into six distinct clusters. Combining molecular and morphological evaluation data eight mutant lines, N10/300/P-2-3-5, N10/300/P-2-3-5, N10/300/P-2-3-5-2, N1/300/P-2-3-5, N1/300/P-2-3-5, N1/250/P-7-6-4-1, N10/300/P-2(1)-4-1 and N1/250/P-7-3-7-1were selected as desired mutant lines having good yield attributing characters and could be recommended for further evaluation in rice breeding program.

Genetic diversity and population structure of enset (Ensete ventricosum Welw Cheesman) landraces of Gurage zone, Ethiopia

Enset (Ensete ventricosum (Welw.) Cheesman), which feeds around 20 million Ethiopian people, is a unique crop; with all parts of the plant are utilizable. It is, arguably, less researched crop and the mode of production remained conventional. Understanding the extent of genetic diversity in the crop, especially making use of genotyping data, is a very important first step in the genetic improvement of the crop. Twelve polymorphic enset SSR markers were used to assess the genetic diversity and population structure of 79 cultivated landraces and four wild enset individuals collected from different enset growing locations of Ethiopia. The polymorphic information content of markers ranged from 0.62 to 0.77 with a mean value of 0.69. A total of 77 alleles were identified, and the average observed heterozygosity varied from 0.51 to 0.67. A mean gene diversity of 0.59 was recorded ranging from 0.55 to 0.62. The AMOVA revealed that within population allelic variations contributed more to the genetic diversity than among population variations. Discriminant Analysis of Principal Components and population structure analysis grouped the 83 enset germplasms into three major clusters, where the wild individuals clustered distinctly. Outcomes of this research provide valuable information for enset conservation and breeding strategies especially for development of resistance for bacterial wilt and nematode attacks.

Genetic characterization and population structure of maize populations using SSR markers

Maize is a major staple food in sub-Saharan Africa. However, due to the threats posed by biotic and abiotic constraints to its production, it is a prerequisite to conserve germplasm with diverse genetic background and to seek for favourable genotypes with such background for improvement of superior genotypes. This study assessed the diversity of 70 white maize populations developed at CSIR-Savanna Agricultural Research Institute with resistance/tolerance to drought and low soil nitrogen (Low-N) using 31 SSR markers. A total of 288 alleles were detected among the germplasm used with a range of 4 to 17 alleles per locus and an average allele number of 9.60 alleles per locus. Polymorphic Information Content values for the SSR markers ranged from 0.32 to 0.85 with a mean value of 0.68. The average heterozygosity obtained from the markers was 0.54 and gene diversity ranged from 0.35 to 0.87 with a mean gene diversity value of 0.71 indicating a high level of polymorphism among the populations. Clustering based on Jaccard's similarity coefficient and an Unweighted Pair Group Method with Arithmetic Mean (UPGMA) revealed 5 clusters for the 70 populations. Evanno method for population structure clustering further revealed two sub-populations. Sub-population 1 was more genetically diverse with an Fst value of 0.18 than sub-population 2 which recorded an Fst value of 0.013. These results indicated that the SSR used were very polymorphic for diversity studies. Also, the studied maize populations are diverse and heterozygous, making them ideal source populations for extraction of drought and low-N tolerant inbred lines.

Evidence of high genetic diversity and significant population structuring in Vachellia tortilis (Forsk.) Galasso & Banfi population in Kenya

High genetic diversity and significant population structure of Vachellia tortilis population in Kenya has been determined using nuclear microsatellite markers. Despite wide distribution and long-distance gene dispersal of the species, geographic barriers affect its gene flow patterns. The Gregorian Rift Valley that cuts across the country is suggested to have differentiated the populations into eastern and western clusters. Vachellia tortilis is an important dryland tree species valued for fuelwood and fodder production; however, no strategy has been put in place for sustainable management of the species genetic resources. Furthermore, there is inadequate information on the species population genetics to aid the development of such strategies. We evaluated the amount and structure of neutral genetic diversity of V. tortilis population in Kenya and provided recommendations necessary for improvement and conservation of the species genetic resources. We hypothesized that the current genetic diversity of V. tortilis is high because of its demographic history and that no population structuring was expected to occur due to the presumed long-distance and effective gene flow patterns within the species. Leaf tissues were collected from 15 putative natural populations of V. tortilis covering the whole distribution range in Kenya. DNA was isolated from the leaf tissues and analyzed using microsatellite markers. In total, 450 trees were genotyped using ten polymorphic nuclear microsatellite loci, and genetic diversity and population structure parameters were determined. We found high levels of genetic diversity within the populations with a mean gene diversity at 0.85. However, significant population differentiation was evident (FST = 0.026, P = 0.007; RST = 0.032, P = 0.004) despite a large number of migrants per generation (Nm = 5.3). Population structure detected suggests the presence of two clusters, although many individuals showed mixed ancestry. The groups reflect the influence of geographic patterns and historical population gene flow. There exists high genetic diversity in V. tortilis in Kenya with significant population structuring into two clusters. We recommend the consideration of the two distinct groups in the development of the species improvement, breeding, and conservation programs. Such programs should ensure maintenance of the majority of the extant genetic diversity.