Genetic landscape of the people of Bangladesh depicted with 17 Y-Chromosome-Specific microsatellites

Gonystylus bancanus (Miq.) Kurz (Thymelaceae) or ramin is an important species producing valuable timber. The existence of this species has now under severe threat due to illegal logging and habitat conversion. Ramin is found only on peat swamp forests, scatteredly distributed in Peninsular Malaysia, Sumatra, and Borneo. Genetic diversity of ramin in the Malesian region has been studied previously for Sumatran populations as well as East and West of Malaysian populations. This present study aimed to determine the genetic diversity and population structures of ramin from Sumatra and Kalimantan using Sequence Random Amplified Polymorphism (SRAP). Five combinations of SRAP primers used to amplify seventy seven samples of ramin from eight populations. Eighty-three putative loci of SRAP were scored and analysed using Popgene and MVSP software. Among eight populations studied, NPL were ranged between 14 – 68 with PPL varied at 16.87 – 81.93%. Number of observed alleles and effective allele numbers were ranged between 1.17 – 1.76 and 1.13 – 1.36 respectively. The lowest gene diversity was accounted for population 2 (He = 0.08) while the highest gene diversity was population 7 and 8 (He = 0.22). The Sumatran and Kalimantan populations were genetically structured at medium level (Gst = 0.25). The pairwise genetic distance among Sumatran and Kalimantan population was considered low (0.04-0.07), and is between Sumatran populations (0.01 – 0.17). The results from this study can be used as an essential information to design conservation strategy for ramin in Indonesia.

Massively parallel sequencing of 24 Y-STR loci in Thai population

Restriction fragment length polymorphism (RFLP) markers were used to assess the genetic structure of populations of Mycosphaerella graminicola collected from wheat fields. A total of 585 isolates representing 10 field populations were sampled from Iran, Argentina and Australia. The genetic structure of M. graminicola populations from Iran and Argentina is described for the first time. Results were compared to previously investigated populations from Israel, Uruguay and Australia. Populations from Iran exhibited high clonality and low gene diversity, suggesting an inoculation event. Populations from uninoculated fields in Argentina had gene and genotype diversities similar to previously described European and North American populations. Genotype diversity was high for populations from Australia and tests for multilocus associations were consistent with sexual recombination in these populations. Gene diversity was low and fixed alleles were found for several loci. These findings are consistent with a relatively small founding population for Australia. These 10 new populations were integrated into a genetic distance comparison with 13 global populations that were characterized earlier.

Napier (Pennisetum purpureum) fodder is an important fodder supporting livestock systems in Bangladesh. Using gamma irradiation we developed 48 Napier fodder mutants which were analyzed through morpho-molecular characterization. Among 48 Napier fodder mutants, 41 mutants were originated by applying radiation (20Gy, 30Gy, 40Gy and 50 Gy) on them. The Napier mutants showed variations in survival rate and fresh weight. The survival rate (0-75%) was observed, 20Gy treated plants produced higher fresh weight in Napier-2, Napier-3, Rokona, Markiron grasses; whereas, 30Gy treated plants produced higher fresh weight in Napier-1, Napier-4 and Pakchong. The total of the alleles found in molecular characterization were 17 and the mean number of allele per locus was 3.4. The PIC value ranged from 0.3047 to 0.6587 having an average of 0.4704 per locus. The highest gene diversity (0.7101) was observed in primer Xipes0093 and the lowest gene diversity (0.3750) was observed in primer PSMP2255, having an average diversity of 0.5286. Pair wise genetic distance values ranged (0.0-1.0) with highest between Napier-2 40 Gy vs (Napier-1control, Napier-2 20Gy Napier-2 30Gy), Napier -3 control, vs (Napier-1control, Napier-2 20Gy Napier-2 30Gy), Napier- 3 20Gy vs (Napier-1control, Napier-2 20Gy Napier-2 30Gy) ,(Napier-3 20Gy, Napier-3 30Gy Napier-1 20Gy, Napier-3 50Gy) vs (Napier -2 20Gy, Napier-3 control, Napier-3 20Gy) etc. The UPGMA displayed five major clusters including sub-clusters. Cluster 5 included the highest number of genotypes (21) and cluster 3 included the lowest number of genotypes (2). The results may be useful for future breeding program for Napier fodder development. SAARC J. Agric., 20(2): 105-119 (2022)

Soil salinity is a major constraint to soybean production. Five soybean genotypes were grown in pots with hydroponic culture under control and different salt stressed conditions to observe salt tolerance capacity on the basis of phenotypic screening and measure genetic diversity and relatedness among the genotypes. Minimum effects of salinity on root and shoot length was observed in Binasoyben-3, GC840 and Binasoyben-5at different salt stresses. Root dry weight and shoot dry weight of different soybean genotypes under different salt stresses were depicted. The highest reduction in root weight was noted in Binasoybean-1. The same genotypes were used to assess genetic diversity among them with simple sequence repeat (SSR) markers. A total of 33 alleles were detected among 5 soybean genotypes by using 10SSR markers. The number of alleles per locus ranged from 2 to 5, with an average of 3.33 alleles across the 10 loci. Rare alleles were observed at 10 SSR loci with an average of 2.8 alleles per locus. In this experiment, two SSR loci were found to be null alleles. The average values of null allele were 0.2. PIC values ranged from 0.27 in Satt184 to 0.77 in Satt339 with the average value of 0.56.The major allele frequency of the most common allele at each locus ranged from 0.80 in Satt184 to 0.20 in Satt339with a mean frequency of 0.48. The size of the different major alleles at different loci ranged from 173 bp for Satt509 to 407 bp for Satt339. The highest gene diversity (0.80) was observed in loci Satt339 and the lowest gene diversity (0.32) was observed in loci Satt184 with the mean diversity of 0.61. The lowest genetic distance (0.60) was observed in Asset vs Binasoybean-3 and Binasoybean-5 vs Binasoybean-3. The highest genetic distance (1.0) was observed between a numbers of genotype pairs with GC840 vs Asset. The UPGMA cluster analysis led to the grouping of the 5 genotypes into two major clusters. GC840, an advanced line identified to be salt tolerant, together with Binasoybean-5 and Binasoybean-3 clustered in the same sub group. The results from morphological and molecular study suggested that GC840 and Binasoybean-3 are moderately tolerant to salt stress.
 Progressive Agriculture 30 (1): 1-9, 2019

Number of grains per panicle is a limiting factor for the yield of aromatic rice. Toovercome this limitation, itmight behelpful to screenaromatic rice using markers linked to grain number.In this study, an elementary DNA fingerprinting database of the nine aromatic rice cultivars was built using four SSR primer pairs linked to Gn1 gene responsible for grain number in rice. For genotyping of aromatic rice cultivars, DNA was extracted from leaf samples using IRRI standard protocol. Allele scoring was done by using a computer based program Alpha Ease FC 4.0 and data were analyzed by Power Marker version 3.25 software. Nei’s genetic distance value and similarity werecomputed. From the analysis, it was found that a total of 21 alleles were detected with an average number of 5.25 alleles per locus having PIC values ranging from 0.3402 (RM5493) to 0.7883 (RM3452) and the average value 0.6629. The highest gene diversity (0.8148) was observed in loci RM3452,and the lowest gene diversity (0.3404) was observed in loci RM5493.From the study, it can be stated that all of the aromatic rice germplasm have bands of the gene that influence the grain but they showed genetic variability.Information obtained from genotyping of varieties helped to analyze the genetic diversity within and among closely related crop varieties which has the potential for crop improvement and to meet the diverse goals like producing cultivars with increased yield of aromatic rice.
 Progressive Agriculture 29 (4): 336-344, 2018

The use of new high-resolution and forensic identification capabilities for population studies offered by new multiplex methods (such as Yfiler Plus) is crucial in forensic genetics cases. The development of haplotype frequency databases is essential to take full advantage of the new Y chromosome determination capabilities. Development of the haplotype database of the Yfiler Plus kit for a population-based sample of 534 males from northeastern Poland and calculation of suitability parameters for forensic genetics studies. The study was conducted on a population sample of 534 unrelated males from the area of northeastern Poland using the Yfiler Plus panel of 27 markers located on the Y chromosome. Four haplotypes appeared twice. The Discrimination Capacity (DC) of the entire set was 0.9925. The highest Gene Diversity (GD) value was calculated for DYS518 (0.86) belonging to the fast-mutation markers, while the lowest GD was calculated for DYS392 (0.42). The results indicate the need for further research and observation of changes, both in different regions of Poland and across Europe.

An isozyme-based assessment of the genetic variability within the <i>Daucus carota</i> complex (Apiaceae: Caucalideae)

Growth characteristics and fertility variations were evaluated at four natural stands of tropical arid zone species, A. leucophloea in southern India. Three stands (TNL 1, TNL 2 and PDM) were situated in dry upland regions while one stand (RKP) was at waterlogged site. The tree height and girth at breast height did not vary between stands in two years. Fertility variation (sibling coefficient, ψ) was estimated based on flowering abundance and fruit set collected for two consecutive years. Fruit production per tree was generally lower in the RKP stand than the other three stands. No year-to-year variation was observed on fruit set in all stands. Growth and flower production showed a weak-positive correlation in both years (R2 = 0.39 to 0.1). The correlation to check if the larger inflorescence size, the higher number of fruit production was also failed. Male fertility variation did not vary much among stands (ψm = 1.28 ~ 1.62). Female fertility variation was low (ψf = 1.71 ~ 2.02) in the three stands situated in dry upland regions than the RKP stand (ψf = 4.09 ~ 4.16). The cumulative contribution of trees to the overall fertility was deviated from the ideal situation (equal contribution) in all stands, especially the RKP stand showed a skewed distribution (R2 ≤ 6.5). The effective population size was low in the RKP predicting a high genetic drift when compared with other sites. Similarly high group coancestry and low gene diversity were observed in the stand RKP. The implications of fertility variation on gene diversity of the species and future management of the natural stands were also discussed.

We have examined variations of five polymorphic loci (DYS287, DXYS5Y, SRY465, DYS19, and DXYS156Y) on the Y chromosome in samples from a total of 1260 males in eight ethnic groups of East Asia. We found four unique haplotypes constructed from three biallelic markers in these samples of East Asians. The Japanese population was characterized by a relatively high frequency of either the haplotype I-2b (-/Y2/T) or II-1 (+/Y1/C). These dual patterns of the distribution of Y chromosomes (I-2b/II-1) were also found in Korea, although they were present at relatively low frequencies. The haplotype II-1 was present in Northeast Asian populations (Chinese, Japanese, Koreans, and Mongolians) only, except for one male from the Thai population among the Southeast Asian populations (Indonesians, Philippines, Thais, and Vietnamese). The Japanese were revealed to have the highest frequency of this haplotype (27.5%), followed by Koreans (2.9%), Mongolians (2.6%), and mainland Chinese (2.2%). In contrast, the frequency of the haplotype I-2b was found to be 17.1% in the Japanese, 9.5% in Indonesian, 6.3% in Korean, 3.8% in Vietnamese, and 2.7% in Thai samples. These findings suggested that the chromosomes of haplotype I-2b were likely derived from certain areas of Northeast Asia, the region closest to Southeast Asia. Phylogenetic analysis using the neighbor-joining tree also reflected a general distinction between Southeast and Northeast Asian populations. The phylogeny revealed a closer genetic relationship between Japanese and Koreans than to the other surveyed Asian populations. Based on the result of the dual patterns of the haplotype distribution, it is more likely that the population structure of Koreans may not have evolved from a single ancient population derived from Northeast Asians, but through dual infusions of Y chromosomes entering Korea from two different waves of East Asians.

Using 15 simple sequence repeat (SSR) microsatellite DNA loci, we analyzed genetic variation within Cocos nucifera germplasm collections at two locations in south Florida, representing eight cultivars. The loci were also used in a parentage analysis of progeny of the 'Fiji Dwarf' variety at both locations. A total of 67 alleles were detected, with eight the highest number at any one locus. These loci identified 83 of the 110 individual palms. Gene diversity of the 15 loci ranged from 0.778 to 0.223, with a mean of 0.574. 'Fiji Dwarf', 'Malayan Dwarf', 'Green Niño' and 'Red Spicata' cultivars resolve as distinct clusters in a neighbor joining tree using modified Rogers distance, while the tall varieties form two aggregates. The highest gene diversity was found in the tall cultivars (H = 0.583 cumulatively), and the lowest in the 'Malayan Dwarf' (H = 0.202). After the tall coconuts, the 'Fiji Dwarf' was most genetically diverse (H = 0.436), and had the largest number of unique alleles. Genetic identity is highest among the 'Malayan Dwarf' phenotypes, and between the tall varieties. The 'Red Malayan Dwarf' is genetically distinct from the 'Green' and 'Yellow Malayan Dwarf' phenotypes, which cannot be distinguished with the SSR loci used. Off-type 'Malayan Dwarf' phenotypes (putative hybrids with talls) can be identified genotypically. Parentage analyses of 30 'Fiji Dwarf' progeny propagated from five adults surrounded by other cultivars estimate that only 20% of the progeny were out-crossed to the other varieties, while 40-46% were possible selfs. This suggests that a seed-production orchard of the variety maintained at reasonable distance from other varieties, will likely yield only 'Fiji Dwarf' genotypes. Our data are discussed in the context of hypotheses of coconut dissemination around the world.

The Kazak ethnic minority is a large ethnic group in the Xinjiang Uygur Autonomous Region of China and is valuable resource for the study of ethnogeny. In the present study, 24 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 201 unrelated Kazak male individuals from Ili Kazak Autonomous Prefecture, Xinjiang, China. The gene diversity of the 24 Y-STR loci in the studied Kazak group ranged from 0.0050 to 0.9104. According to haplotypic analysis of the 24 Y-STR loci, 113 different haplotypes were obtained, 96 of which were unique. The haplotype diversity and discrimination capacity in Kazak group were 0.9578 and 0.5622 at 24 STR loci, respectively. The haplotype diversity and discrimination capacity at Y-filer 17 loci, extended 11 loci, and minimal 9 loci were reduced to 0.9274 and 0.4279, 0.8459 and 0.3284, and 0.8354 and 0.2985, respectively, which could indicate that the more loci were detected, the higher forensic efficacy was obtained. We evaluated the application value of the 24 loci in forensic sciences and analyzed interpopulation differentiations by making comparisons between the Kazak1 (represent our samples from Ili Kazak Autonomous Prefecture) group and other 14 groups. The results of pairwise genetic distances, multidimensional scaling plot, and neighbor-joining tree at the same set of 17 Y-filer loci indicated that the Kazak1 group had the closer genetic relationships with Kazak2 (represent samples from the whole territory of Xinjiang Uygur Autonomous Region), Mongolian, and Uygur ethnic groups. The present results may provide useful information for paternal lineages in forensic cases and can also increase our understanding of the genetic relationships between Kazak1 and other groups.

AimTo investigate the distribution of 17 Y-short tandem repeat (STR) loci in the population of the Cukurova region of Turkey.MethodsIn the period between 2009 and 2010, we investigated the distribution of 17 Y-STRs in a sample of 249 unrelated healthy men from the Cukurova region of Turkey. Genomic DNA was extracted with InstaGene matrix and Y-STRs were determined using the AmpFISTR Yfiler PCR amplification kit. Gene and haplotype diversity values were estimated using the Arlequin software. To compare our data to other populations, population pairwise genetic distances and associated probability values were calculated using the Y Chromosome Haplotype Reference Database Web site software.ResultsAt 17 Y-STR loci we detected 148 alleles. The lowest gene diversity in this region was 0.51 for DYS391 and the highest 0.95 for DYS385a/b. Haplotype diversity was 0.9997 ± 0.0004. We compared our data with haplotype data of other Turkish populations and no significant differences were found, except with Ankara population (Φst = 0.025, P = 0.018). Comparisons were also made with the neighboring populations using analysis of molecular variance of the Y-STR loci genetic structure and our population was nearest to Lenkoran-Azerbaijani (Φst = 0.012, P = 0.068) and Iranian Ahvaz population (Φst = 0.007, P = 0.173), followed by Greek (Φst = 0.026, P = 0.000) and Russian (Φst = 0.048, P = 0.000) population. Other countries like Portugal, Spain, Italy, Egypt, Israel (Palestinian Authority Area), and Taiwan showed a high genetic distance from our population.ConclusionOur study showed that Y-STR polymorphisms were a powerful discrimination tool for routine forensic applications and could be used in genealogical investigations.

Litchi (Litchi chinensis Sonn.) is an introduced crop in India and has limited genetic variability characterized by differences in flushing pattern, leaf, panicle and fruit traits. Molecular markers were employed to expose the genetic diversity of 20 litchi cultivars from the Indian peninsula and facilitate documentation of the native germplasm diversity. Efficiency of individual primers was evaluated on the basis of average band informativeness and resolving power, where random oligonucleotide markers OPA-5 and OPA-3 scored best. Among tested microsatellite markers, ISSR 01 and 13 had high values for primer efficiency and these were found to supplement simple sequence repeats for generation of cultivar barcode and clustering analyses. Efficiency of microsatellites (Simple Sequence Repeats and Inter Simple Sequence Repeats) was established by high values for polymorphism (0.691), diversity index (0.264), effective multiplex ratio (48.8470) and marker index (12.896), thus reiterating its potential as for developing barcodes for cultivar identification and conservation. Phylogenetic analysis based on RAPD and microsatellites revealed clustering of the cultivars into four major groups, although within a very narrow range (0.63 - 0.90) of similarity, viz. Seedless (i.e. Bedana), Mandarji, Shahi and China groups. The clustering followed grouping based on fruit morphology, leaf and panicle attributes disagreeing with earlier views regarding incongruity of clustering pattern with morphological, ecological and climatic adaptations. Discrimination of cultivars like Dehrarose and Dehradun, being often labeled as synonyms, was also done. Interestingly high polymorphism and low gene diversity have been exposed by molecular markers, commenting on narrow genetic background of litchi cultivars from India.

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.