Mean Gene Diversity Research Articles

Genetic diversity analysis of tropical and sub-tropical maize germplasm for Striga resistance and agronomic traits with SNP markers.

Striga hermonthica (Sh) and S. asiatica (Sa) are major parasitic weeds limiting cereal crop production and productivity in sub-Saharan Africa (SSA). Under severe infestation, Striga causes yield losses of up to 100%. Breeding for Striga-resistant maize varieties is the most effective and economical approach to controlling the parasite. Well-characterized and genetically differentiated maize germplasm is vital to developing inbred lines, hybrids, and synthetic varieties with Striga resistance and desirable product profiles. The objective of this study was to determine the genetic diversity of 130 tropical and sub-tropical maize inbred lines, hybrids, and open-pollinated varieties germplasm using phenotypic traits and single nucleotide polymorphism (SNP) markers to select Striga-resistant and complementary genotypes for breeding. The test genotypes were phenotyped with Sh and Sa infestations using a 13x10 alpha lattice design with two replications. Agro-morphological traits and Striga-resistance damage parameters were recorded under a controlled environment. Further, high-density Diversity Array Technology Sequencing-derived SNP markers were used to profile the test genotypes. Significant phenotypic differences (P<0.001) were detected among the assessed genotypes for the assessed traits. The SNP markers revealed mean gene diversity and polymorphic information content of 0.34 and 0.44, respectively, supporting the phenotypic variation of the test genotypes. Higher significant variation was recorded within populations (85%) than between populations using the analysis of molecular variance. The Structure analysis allocated the test genotypes into eight major clusters (K = 8) in concordance with the principal coordinate analysis (PCoA). The following genetically distant inbred lines were selected, displaying good agronomic performance and Sa and Sh resistance: CML540, TZISTR25, TZISTR1248, CLHP0303, TZISTR1174, TZSTRI113, TZDEEI50, TZSTRI115, CML539, TZISTR1015, CZL99017, CML451, CML566, CLHP0343 and CML440. Genetically diverse and complementary lines were selected among the tropical and sub-tropical maize populations that will facilitate the breeding of maize varieties with Striga resistance and market-preferred traits.

Molecular marker-assisted genetic diversity analysis in soybean cultivars from Himalayan region of Uttarakhand, India

‘Bhat’ is the soybean variety highly valued in the traditional food and therapeutic system of Uttarakhand state in the Indian Himalayan region. It is available in diverse colors, shapes, and sizes, often linked to their nutritional parameters. The present investigation was conducted to assess the diversity and genetic relatedness in ‘bhat’ genotype indigenous to the Garhwal division of Uttarakhand. 25 polymorphic simple sequence repeats (SSR) markers were used to determine the genetic diversity and varietal identification among the 45 genotypes collected from the different villages of Uttarakhand. Out of the different markers assessed only 13 primers showed amplification with the maximum of 2–4 alleles obtained with each primer with the molecular weight ranging between 80 and 400 kb. The highest band amplification was observed in Satt 257 and Satt 197. The allelic frequencies of amplified primers ranged from 0.5 to 0.833 with a mean value of 0.645 and the mean gene diversity and PIC value was found to be 0.43 and 0.33. Satt 183, Satt 288, and Satt 389 showed the highest polymorphism, while Satt257 and Satt245 exhibited the presence of unique alleles in some samples. The phylogenetic analysis grouped the genotypes into 4 major clusters having visually distinct phenotypes in each group, indicating the mixing of population and loss of authenticity also confirming that phenotypic attributes are not indicative of genetic relatedness among the genotype under study. The results indicate the need for the development of novel ‘bhat’ specific markers for more accurate genetic identification of the nutritionally rich indigenous soybean variety.

Genetic variation among Brassica rapa subsp. rapa genotypes growing in Malatya/Türkiye

In this study, the genetic variation of 18 Brassica rapa subsp. rapa genotypes grown in Malatya was determined using the inter simple sequence repeat - polymerase chain reaciton (ISSR-PCR). Using nine ISSR primers, a total of 73 bands were obtained and the polymorphism rate was 91.78%. The mean polymorphism information content value was determined as 0.3319. The mean gene diversity (H) value was determined as 0.4276. The mean major allele frequency value was determined as 0.6531. Similarity index values were determined to be between 0.0928 and 1.0924. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram consisted of two groups. Principal component analysis analysis and UPGMA dendrogram were compatible. In addition, the groups in the phylogenetic trees were partially compatible with geographical distribution. Our results suggest that ISSR-PCR analysis is a suitable approach for breeding Brassica rapa subsp. rapa genotypes and developing different cultivars.

Genetic Relationships of Indigenous King Coconut (Cocos nucifera L.) Populations as Determined by SSR Markers

King Coconut (KC) is an indigenous and highly valuable germplasm resource in Sri Lanka. Yet, KC populations' genetic diversity, relationships, and conservation strategies are not fully understood. Indigenous old KC populations have been dispersed across a few ancient villages in Sri Lanka. Five geographically dispersed locations were selected in Sri Lanka, and 20 KC individuals from each location were collected for the current study. Six randomly selected samples from every geographical location, together with the standard two Sri Lanka Red Dwarf and two Sri Lanka Tall varieties were initially genotyped using 21 SSR markers for polymorphism. Based on the results, ten polymorphic SSR markers were selected and used for genotyping. Power Marker, STRUCTURE, and GenAlex software were used for the SSR genetic analysis. Results revealed 0.62 mean Gene Diversity (Hs), 4.2 mean allele number, and 0.55 polymorphic information content (PIC). Clear differentiation of populations was observed with the STRUCTURE and UPGMA dendrogram. Single branching in the UPGMA dendrogram for Anuradhapura and Marandawila KC populations revealed high genetic uniformity over multi-branched Kadugannawa and Colambageara populations. According to AMOVA, 64% of the genetic variation has been partitioned among populations, indicating moderate population differentiation. Detail analysis, including a higher number of KC populations and systematic molecular analysis using more SSRs/SNPs needed in the future before implementing conservation and utilization strategies.

Genetic diversity and population structure of maize inbred lines using phenotypic traits and single nucleotide polymorphism (SNP) markers

Understanding germplasm’s genetic diversity is essential for developing new and improved cultivars with stable yields under diverse environments. The objective of this study was to determine the genetic diversity and population structure of 128 maize inbred lines sourced from the International Institute of Tropical Agriculture (IITA), the International Maize and Wheat Improvement Centre (CIMMYT), and the University of KwaZulu-Natal (UKZN) using 11,450 informative single nucleotide polymorphism (SNP) markers. The inbred lines revealed highly significant (p < 0.001) levels of variability for the key phenotypic traits. The SNP markers had a mean gene diversity (GD) and polymorphic information content (PIC) of 0.40 and 0.31, respectively, indicating the existence of substantial genetic variation across the germplasm panel. The model-based population structure analysis identified three subpopulations (K = 3) among the inbred lines. This corroborated the phylogenetic analysis using phenotypic traits and molecular markers which classified the inbred lines into three groups. The findings of this study identified considerable genetic diversity for the selection of inbred lines with favourable alleles for multiple traits and could be useful to initiate marker-assisted selection (MAS) to identify significant loci associated with agronomic performance and multiple-stress tolerance.

RAPD MARKERS BASED GENETIC DIVERSITY ANALYSIS OF ONION (ALLIUM CEPA) GERMPLASM

Onion is one of the most popular spice crop, which is used for seasoning wide range of dishes as well as folk medicine. Assessment of genetic diversity helps to use the onion germplasm as breeding materials for its improvement. Molecular marker based diversity assessment is more powerful, rapid and reliable compared to morphology based genetic diversity assessment. Thirty eight onion germplasm were characterized by using 10 random amplied polymorphic DNA (RAPD) markers for estimating genetic diversity within the germplasm. The germplasm exhibited wide range of variability which could be used in cross breeding for getting superior F1 generation. Out of 10 primers, four gave polymorphism among onion germplasm. Genetic diversity of 38 germplasm was analyzed using variation at 34 RAPD loci, of which 91.89% were polymorphic. The highest pair wise genetic distance was 1.046 and the lowest was 0.056. The mean gene diversity among all the germplasm was 1.54 and Shannon's information index was 0.3188. The UPGMA dendrogram, based on Nei`s genetic diversity showed 6 clusters. The frequency of polymorphic loci ranged from 0.0263 to 1.0000, indicates that there exists a wide genetic diversity among the germplasm and corroborated the usefulness of RAPD markers for estimating genetic diversity in onion.

Molecular Characterization of Tinospora cordifolia (Willd.) Miers Using Novel g-SSR Markers and Their Comparison with EST-SSR and SCoT Markers for Genetic Diversity Study.

In the present study, novel genomic-SSR (g-SSR) markers generated in our laboratory were used to characterize Tinospora cordifolia and related species. The g-SSR marker was also compared with EST-SSR and SCoT markers used earlier in our laboratory to assess the genetic diversity of T. cordifolia. A total of 26 accessions of T. cordifolia and 1 accession each of Tinospora rumphii and Tinospora sinensis were characterized using 65 novel g-SSR markers. A total of 125 alleles were detected with 49 polymorphic g-SSR markers. The number of alleles per locus varied from 1-4 with a mean value of 2.55 alleles per locus. Mean PIC, gene diversity, and heterozygosity were estimated to be 0.33, 0.41, and 0.65, respectively. The two species, namely T. rumphii and T. sinensis, showed cross-species transferability of g-SSRs developed in T. cordifolia. The success rate of cross-species transferability in T. rumphii was 95.3% and 93.8% in T. sinensis, proving the usefulness of this marker in genetic diversity studies of related species. The Tinospora accessions were also used for molecular characterization using SCoT and EST-SSR markers and compared for genetic diversity and cross-species transferability. The PIC, gene diversity, heterozygosity, and principal coordinate analysis showed that g-SSR is the better maker for a genetic diversity study of T. cordifolia. Additionally, high cross-species transferability of g-SSRs was found (95.3% and 93.8%) compared to EST-SSRs (68.8% and 67.7%) in T. rumphii and T. sinensis, respectively.

Genetic diversity and grouping of pigeonpea [Cajanus cajan Millspaugh] Germplasm using SNP markers and agronomic traits.

Knowledge of genetic interrelationships and grouping among pigeonpea germplasm collections is fundamental to selecting breeding parents with unique genetic constitutions. The objectives of this study were to assess the genetic diversity and genetic grouping present among 81 pigeonpea genotypes collected from Malawi, Tanzania and Kenya using 4122 single nucleotide polymorphism (SNP) markers and complementary morphological traits. The SNP markers and phenotypic traits revealed significant genetic variation among the assessed genotypes. The test genotypes were resolved into three distinct clusters based on both marker systems. The mean gene diversity and the polymorphic information content (PIC) were 0.14 and 0.11, suggesting moderate genetic differentiation among the genotypes. The analysis of molecular variance revealed that differences among populations accounted for only 2.7% of the variation, while within the population (among individuals) accounted for 97.3% of the variation. The results based on the DArT SNP genotyping complemented the phenotypic data and led to the selection of unique pigeonpea genotypes for effective breeding programs in Malawi and related agroecologies. This suggested that unique breeding populations could be created by identifying and selecting divergent individuals as parental lines. There is a need to create a new genetic variation or introgress genes from genetically unrelated parents to increase the genetic base of the current pigeonpea breeding populations.

Assessment of Genetic Diversity in Plantain (Musa paradisiaca L) Using Yield-Related Agro-Morphological Traits and Microsatellite Markers

Background and Objective: Plantain (Musa paradisiaca L) remains one of themost important staple food crop and perhaps, one of the oldest cultivated fruit tree crop in the humid tropics of Africa, Central Asia, South America and the West Indies.Fourteen (14) elite plantain cultivars were evaluated for genetic diversity using agro-morphological yield related attributes and simple sequence repeat (SSR) markers.&#x0D; Materials and Methods: Six (6) microsatellite markers that showed distinct fragments varying from 50 bp to 3.0 Kbp in size of polymorphic bands were selected and used for molecular characterization and fingerprinting, while agro-morphological (yield–related) attributes assessed included bunch weight, number of hands/bunch, number of fingers/hands, number of fingers/bunch, harvest interval, length of plant cycle, pulp hardness and pulp to skin weight ratio of the elite plantain cultivars.&#x0D; Results: The total number of amplified bands (TNB), mean percentage polymorphism (%P), mean polymorphic information content (PIC), average marker index (MI) and mean gene diversity for the SSR assay were 59, 70.24%, 0.79, 3.74 and 0.832 respectively. Results of agro-morphological fingerprint study revealed a significant variations in terms of the bunch weight, number of finger per hands/bunch, number of fingers per hand, number of fingers /bunch, harvest interval, length of crop cycle, pulp hardness and pulp/wt. ratio all showed significant variations among the cultivars. The distribution of the elite cultivars along with the principal components showed cluster pattern of distribution within the study location. Principal component analysis revealed four principal components contributing 99.91% to the observed morphological variations while analysis of molecular variance revealed 96.00% contributed by molecular characteristics to observed variations. The yield displayed revealed significant contributions of bunch weight, fingers/hand and fingers/bunch as the main indices for plantain yield. The dendrograms for both morphological and molecular characteristics delineated the cultivars into four distinct cluster groups and subgroups each varying in genetic distance.&#x0D; Conclusion: These good cultivars can be exploited for the improvement of low yielding cultivars in other region to increase and improve plantain yield, promote food security and income generation especially under the present economic realities where food security is threatened by the global food crises and declining crop productivity.

Detection of Genomic Regions Controlling the Antioxidant Enzymes, Phenolic Content, and Antioxidant Activities in Rice Grain through Association Mapping.

Because it is rich in antioxidant compounds, the staple food of rice provides many health benefits. Four antioxidant traits in rice grain, viz., catalase, CUPRAC, DPPH, FRAP and peroxidase, were mapped in a representative panel population containing 117 germplasm lines using 131 SSR markers through association mapping. Donor lines rich in multiple antioxidant properties were identified from the mapping population. The population was classified into three genetic groups and each group showed reasonable correspondence with the antioxidant traits. The presence of linkage disequilibrium in the population was confirmed from the estimated Fst values. A strong positive correlation of DPPH was established with TPC, FRAP and CUPRAC. A moderate to high mean gene diversity was observed in the panel population. Eleven significant marker-trait associations for antioxidant traits were mapped, namely, qACD2.1, qACD11.1 and qACD12.2 for DPPH; qCAT8.1 and qCAT11.1 for catalase; qFRAP11.1, qFRAP12.1 and qFRAP12.2 for FRAP; and qCUPRAC3.1, qCUPRAC11.1 and qCUPRA12.1 regulating CUPRAC. Co-localization of the QTLs for qACD11.1, qFRAP11.1 and qCUPRAC11.1 were detected, which may act as antioxidant hotspots regulating DPPH, FRAP and CUPRAC activities, respectively, while qACD12.2 and qFRAP12.1 remained close on the chromosome 12. These detected QTLs will be useful in antioxidant improvement programs in rice.

Revealing genetic structure in the paternal lineages and forensic profiling of Bhotra tribe by the analysis of Y-STR multiplex platform

India has a diverse reservoir of genetic components, ethnicity and linguistic affiliations. Y-STR (Short Tandem Repeat) markers serve as a potential tool in the fields of anthropological genetics, ancestry exploration, as well as in forensic investigations. The present study was conducted to explore the molecular diversity in respect to male lineage, genomic heritage and forensic profiling of Bhotra tribe of Odisha, India, by using 23 Y-STR molecular markers. Blood samples were collected randomly from 133 unrelated healthy adult male individuals of Bhotra population following the ethical standards.Out of 133 individuals, 109 unique haplotypes were observed. Discrimination Capacity (DC) was observed at 0.8195; mean Gene Diversity (GD) was observed to be 0.615 along with the Standard Error (SE) of 0.027. The locus DYS385a/b showed the highest genetic diversity (0.887). To assess the genetic affinity of the Bhotra population with other Indian population that were reported to Y-STR Haplotype Reference Database (YHRD) before, Multidimensional Scaling plot (MDS), Neighbor Joining (NJ) tree, and Principal Coordinate Analysis (PCoA) were performed. The study population exhibited a high degree of genetic diversity and indicated genetic affinity with the Majhi and Dorla tribes of Chhattisgarh. Study population characterized by 12 different haplogroups and H1a1a (33.03%) was the most frequently observed haplogroup, indicating the ancestral relationship of Bhotra with the European Romani population.To the best of our knowledge, this is the first global report of the genetic diversity of the Bhotra tribe on 23 Y STR genetic markers, which would be profoundly useful in forensic investigation, medical, and anthropological studies and would also enrich the Indian Y-STR database.

Analyses of genetic diversity and population structure of sesame (Sesamum indicum L.) germplasm collections through seed oil and fatty acid compositions and SSR markers

Knowledge of the genetic profiles of diverse germplasm collections of sesame using seed oil, fatty acid contents, and molecular markers is a prerequisite to develop market-preferred cultivars with quantity and quality oil. The objective of this study was to determine the genetic diversity and relationships among Ethiopia’s sesame germplasm collections using seed oil content and fatty acid compositions and diagnostic simple sequence repeat (SSR) markers to select genetically complementary and promising parental lines for breeding. The contents of the seed oil and fatty acids of 100 lines grown under field conditions were determined using the near-infrared reflectance spectrometry. Twenty-seven polymorphic SSR markers were used to assess the genetic profile of the test lines and complement the seed oil and fatty acid data. The SSR markers revealed that the mean gene diversity and polymorphic information content were 0.30 and 0.25, respectively. Population structure analysis identified four major heterotic groups. Based on higher oil content and desirable fatty acid compositions and SSR markers the following superior and complementary lines such as: Hirhir Kebabo Hairless Sel-6 (from sub-cluster I-b), Hirhir Humera Sel-8 and NN0058–2 (sub-cluster II-a) and Bawnji Fiyel Kolet (sub-cluster II-b) are identified for sesame breeding programs or production globally.

Genetic variation for grain phytate and molecular characterization of low phytic acid‐2 (lpa2) gene‐based maize (Zea mays) inbreds

AbstractMaize possesses higher concentration of phytic acid (PA) compared with other cereals, reducing bioavailability of iron and zinc. Reduction of PA in maize grains thus assumes significance to alleviate micronutrient malnutrition. Here, a set of 24 inbreds possessing mutant lpa2‐1 gene and seven inbreds with wild‐type LPA2 gene was field evaluated at Delhi and Hyderabad. The performance of lpa2‐1‐based inbreds was at par with wild‐type inbreds for grain yield (P = .09645) and key agronomic traits (P &gt; .54100). Mutant inbreds possessed significantly low mean PA (1.90 mg/g) over wild‐type inbreds (2.56 mg/g) (P &lt; .00001), with average reduction of 26% PA among lpa2‐1 mutants. Mean inorganic phosphorous (iP) was 0.81 mg/g in lpa2‐1 mutants and 0.27 mg/g in wild types, revealing significantly (P &lt; .00001) higher increment (three‐fold) of iP in mutants compared with wild‐type inbreds. Characterization using 61 simple sequence repeats (SSRs) generated 181 alleles with mean polymorphism information content of 0.40 and mean gene diversity of 0.46. Cluster analyses grouped lpa2‐1 inbreds into three‐major clusters. The study identified potential cross combinations for development of low phytate maize with higher bioavailability of iron and zinc.

Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers.

In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.

Estimation of Genetic Diversity among Canola Accessions using Simple Sequence Repeat Markers

Genetic studies through molecular markers proved important to find out the genetic diversity of canola. In this study, 50 lines of canola were used to find the polymorphism using 15 SSR primers and investigated the genetic diversity, PIC values, frequency-based genetic distance, and allelic frequencies. Mean gene diversity, frequency-based genetic distance, and PIC values were 0.8777, 0.233 and 0.8666, respectively for the canola lines. A good range of genetic diversity was found among studied canola lines with value 85.91% polymorphism. Maximum and minimum genetic distances among 50 lines were 1 and 0.26, respectively. Accessions ACC-26068, ACC-24241, ACC-24244, ACC-24233, ACC-24423 and ACC-24224 have maximum genetic distance. Accessions ACC-24879 and ACC-24169 had minimum genetic distance i.e., 0.26. Dendrogram based on genetic distances showed four main clusters that were further dividing into several sub-clusters. The primers utilized in the present study, were valuable to identify different accessions of canola to find the variability present. This variability will be helpful to initiate the breeding program with their molecular genetic basis.

Genetic diversity of mangrove tree species Avicennia marina in eco-geographic regions of Kerala coast, Southern India

The genetic assembly of Avicennia marina (Forsk.) Vierh, Avicenniaceae within and between the three natural mangrove forests of Kerala coast belonging to the districts of Kochi, Kozhikode and Kannur was investigated using Inter Simple Sequence Repeat (ISSR) markers to provide coherent scientific conservation practices. The ten selective ISSR primer combinations of 60 genotypes of Avicennia marina ensured a total of 171 bands of which 84.5% were polymorphic. Gene diversity index H varied from 0.142 Kochi to 0.195 Kozhikode. The mean gene diversity H S was 0.169 and the total gene diversity H T was 0.262 which showed a moderate level of genetic diversity in the studied population. The mangrove Avicennia marina populations showed large genetic difference G ST = 0.3849, indicating that 38% of the total genetic diversity was among the populations and the rest 62% resides within the population. The gene flow estimates Nm = 0.79 shown that natural mangroves of Kerala are in the course of differentiation due to genetic drift. We investigated the genetic distinctiveness of taxonomically confusing species, Avicennia marina and Avicennia officinalis , and resulted in clear demarcation between the two. There is a significant correlation between dendrogram and PCoA designated that extensive distant spreading of seeds between populations of Avicennia marina is comparatively low. The genetic study contributed relatively high diversity and strong differentiation across the three eco-geographic locations. The best remedy to preserve coastal mangrove species like Avicennia marina is to plant the identical species in its respective habitat. Launch, on-site protection zones to safeguard the species and to decrease the impact of human activities would allow its habitats to increase in size through natural regeneration.

Genetic Diversity and Population Structure of Didymellarabiei Affecting Chickpea in Ethiopia.

Ascochyta blight, also known as chickpea blight, which is caused by the fungal pathogen, Didymella rabiei, is an important disease affecting chickpea (Cicer arietinum L.) in many countries. We studied the genetic diversity and population structure of 96 D. rabiei isolates collected from three geographic populations in Ethiopia using simple sequence repeat (SSR) markers. We confirmed the genetic identity of 89 of the D. rabiei isolates by sequencing their rRNA internal transcribed spacer region genes. The chickpea blight pathogen isolates were genetically diverse, with a total of 51 alleles identified across 6 polymorphic SSR loci, which varied from 3 to 18 (average 8.5) alleles per SSR marker. The observed heterozygosity and expected heterozygosity ranged from 0.01 to 0.92 and 0.19 to 0.86, respectively. The mean polymorphic information content value of the D. rabiei populations was 0.58, with a mean gene diversity of 0.61 among loci. Gene flow (Nm = number of migrants) for the three populations of D. rabiei isolates ranged from 1.51 to 24.10 (average 6.2) migrants/cluster. However, the genetic variation between the D. rabiei populations was small (8%), with most of the variation occurring within populations (92%). Principal component analysis to visualize genetic variation showed that the D. rabiei isolates obtained from most of the chickpea samples formed roughly three groups on a two-dimensional coordinate plane. Similarly, the clustering of individuals into populations based on multi-locus genotypes (using Clumpak) grouped isolates into three clusters but with individual isolate admixtures. Hence, no clear geographic origin-based structuring of populations could be identified. To our knowledge, this is the first report of D. rabiei diversity in Ethiopia. Virulence studies should be conducted to develop chickpea varieties that are resistant to more aggressive pathogen populations.

Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars.

Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (FST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.

Phylogenetic Analysis and Genetic Diversity of Colletotrichum falcatum Isolates Causing Sugarcane Red Rot Disease in Bangladesh.

Simple SummarySugarcane is an important agro-industrial crop because it is one of the major sources of white sugar. Red rot which is caused by Colletotrichum falcatum is the most devastating disease of sugarcane because its infestation results in significant sugarcane yield loss. The intra- and inter-specific genetic diversity, population structure and phylogenetic relationship amongst C. falcatum isolates from Bangladesh remain unclear. This information is essential for the effective management of red rot and to also develop resistant sugarcane varieties through plant breeding programmes. This paper demonstrates the phylogenetic relationship and genetic diversity of C. falcatum isolates from Bangladesh. Also, it provides baseline information that can be used to establish red rot disease management strategies for future application.Colletotrichum falcatum Went causes red rot disease in sugarcane farming in the tropical and sub-tropical regions. This disease causes significant economic loss to the sugarcane production industry. Successful disease management strategies depend on understanding the evolutionary relationship between pathogens, genetic diversity, and population structure, particularly at the intra-specific level. Forty-one isolates of C. falcatum were collected from different sugarcane farms across Bangladesh for molecular identification, phylogeny and genetic diversity study. The four genes namely, ITS-rDNA, β-tubulin, Actin and GAPDH sequences were conducted. All the 41 C. falcatum isolates showed a 99–100% similarity index to the conserved gene sequences in the GenBank database. The phylogram of the four genes revealed that C. falcatum isolates of Bangladesh clustered in the same clade and no distinct geographical structuring were evident within the clade. The four gene sequences revealed that C. falcatum isolates from Bangladesh differed from other countries´ isolates because of nucleotides substitution at different loci. The genetic structure of C. falcatum isolates were determined using ISSR marker generated 404 polymorphic loci from 10 selected markers. The percentage of polymorphic loci was 99.01. The genetic variability at species level was slightly higher than at population level. Total mean gene diversity at the species level was 0.1732 whereas at population level it was 0.1521. The cluster analysis divided 41 isolates into four main genetic groups and the principal component analysis was consistent with cluster analysis. To the best of our knowledge, this is the first finding on characterizing C. falcatum isolates infesting sugarcane in Bangladesh. The results of this present study provide important baseline information vis a vis C. falcatum phylogeny analysis and genetic diversity study.

Genetic and molecular characterisation of subtropically adapted low-phytate genotypes for utilisation in mineral biofortification of maize (

Phytic acid (PA) is a major anti-nutritional factor in maize grains and significantly reduces the bioavailability of minerals such as iron and zinc in humans. Reduction of PA in maize (Zea mays L.) thus assumes great significance. Despite the availability of low phytic-acid (lpa) mutants in maize, their utilisation in breeding has been limited because of non-availability of well adapted lpa-based inbreds. A set of 24 subtropically adapted lpa1-1-based maize inbreds derived through molecular breeding was evaluated along with seven wild-type inbreds at multilocation. The lpa1-1 inbreds possessed 35.8% lower PA (1.68 mg/g) than the wild-type inbreds (2.61 mg/g). Mean proportion of PA was lower in the lpa1-1-based inbreds (62.8%) than in the wild-type inbreds (91.6%). The lpa1-1 inbreds showed similar performance for plant- and ear-height besides flowering behaviour as did wild types. Average grain yield among lpa1-1 inbreds (2735.9 kg/ha) was at par with the original versions (2907.3 kg/ha). Molecular profiling of these lpa1-1 inbreds using 60 genome-wide single-sequence repeats generated 172 alleles, with a mean of 2.87 alleles per locus. Mean polymorphism information content and mean gene diversity were 0.41 and 0.48 respectively. Genetic dissimilarity ranged from 0.23 to 0.81, with an average of 0.64. Cluster analyses grouped 24 lpa1-1 genotypes into three major clusters, and principal-coordinate analysis depicted the diverse nature of genotypes. The study also identified a set of potential hybrid combinations with low PA for their direct utilisation in biofortification program. This is the first study on comprehensive characterisation of lpa1-1-based inbreds adapted to subtropical conditions.