The study aimed to assess the genetic diversity of 2-decyl-4-quinazolinyl amine exon2 (DQA2 exon2) gene among the Egyptian goat populations from different agro-climatic areas. Data of diseases distribution as well as blood samples were collected. The data collected for diseases distribution showed differences in the types of diseases between the agro-climatic areas. The Single Strand Conformation Polymorphism technique (SSCP) was used to assess the genetic diversity of DQA2 exon2 gene among the goat populations. The results showed that the DQA2 exon2 gene locus displayed 21 alleles with different frequencies in each of goat population. The gene diversity values among the populations ranged from 0.950&plusmn; 0.022 to 0.887&plusmn; 0.033. The difference between the most southern population (Aswan) and the remaining populations translate to significant (P&lt; 0.05) differentiation for only one population pair (Aswan &ndash; Baladi, with FST= 0.055; P= 0.001). Scrutiny of allele composition in these two goat populations showed unique alleles in each population (six in Aswan and four in Baladi). The results of the study suggested that the allelic numbers and allelic composition for the DQA2 exon2 gene among the Egyptian goat populations showed diversity in the immune gene due to the different pathogens exposure.

Allelic diversity of DQA2 exon 2 gene in Egyptian goat populations

<div>Background:&nbsp;Many genetic variants of beta-casein in different breeds of cattle have been reported. The A1 and A2 are the most common variants. The breeds of Zebu cattle have high frequency of A2 allele or monomorphic for A2 allele. The current study aimed to screen Indian Zebu cattle breeds, Bargur and Umblachery, for A1 and A2 alleles at beta-casein locus. 
 
Methods:&nbsp;A total of 48 Bargur and 42 Umblachery cattle were genotyped for &beta;-casein (CSN2) gene using allele-specific PCR. The gene and genotype frequencies were estimated. The theoretical heterozygosity (Heexp), experimental heterozygosity (Heobs), polymorphism information content (PIC), expected homozygosity (E), effective number of alleles (ENA) and level of possible variability realization (V%) were calculated. 
 
Result:&nbsp;The investigation revealed the presence of both A1 and A2 alleles at beta-casein locus in both Bargur and Umblachery cattle breeds. The A1A1 genotype was not observed in both the breeds. The frequencies of A1A2 and A2A2 genotypes were 0.125 and 0.875 respectively in Bargur and 0.050 and 0.950 respectively in Umblachery breed. The study indicated the predominance of A2 variant in both the breeds. The frequencies of A1 and A2 alleles were 0.063 and 0.937 respectively in Bargur and 0.02 and 0.98 respectively in Umblachery breed. The values of experimental heterozygosity (Heobs), theoretical heterozygosity (Heexp), polymorphism information content (PIC), expected homozygosity (E), effective number of alleles (ENA), level of possible variability realization (V%) were 0.125, 0.1163, 0.1095,0.8837, 1.131 and 11.88 respectively in Bargur breed. These values were 0.048, 0.0468, 0.0458, 0.9532, 1.049 and 4.79 respectively in Umblachery population. The observed heterozygosity and PIC values revealed the existence of very low genetic variability in the tested populations. The present work will be a contribution to the study on beta-casein locus in Indian zebu cattle.</div>

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Detection of A1 and A2 Alleles at Beta-casein Locus in Bargur and Umblachery (Indian Zebu) Cattle Breeds by Allele-specific PCR

<div>Background: The variety of indigenous duck germplasm contribute maximum to the poultry industry in India, besides chicken population. In southern part of India, the available duck genetic resource, particularly Arni ducks (comprises of Sanyasi and Keeri ducks) of Tamil Nadu, has its own characteristics with innate potentiality of higher productivity without any input system of management. Genetic characterization and diversity of indigenous duck genetic resources has not been properly studied. In the present study, the genetic diversity of Arni ducks with other indigenous and exotic duck germplasm were analysed with microsatellite markers.&nbsp; 
 
Methods: Genomic DNA was isolated from the blood samples of six duck populations. Molecular characterization was carried out with duck specific FAO recommended microsatellite markers. The genotyping of ducks was done based on the size of 4324 PCR amplicons of 23 microsatellite loci, which were subjected to capillary electrophoresis using automatic sequencer. 
 
Result: A total of 222 alleles in six duck populations across 23 microsatellite loci with a mean of 9.65&plusmn;0.95 alleles were found. Kuttanad duck variety had the highest number of alleles (139) followed by Sanyasi (136), Keeri (129), Muscovy (118), Assam (91) and White Pekin (78) ducks. The mean observed number of alleles was 6.04&plusmn;0.59, 5.91&plusmn;0.76, 5.61&plusmn;3.17, 5.13&plusmn;0.44, 3.96&plusmn;0.76 and 3.39&plusmn;0.40 in Kuttanad, Sanyasi, Keeri, Muscovy, Assam and White Pekin ducks respectively. The overall mean polymorphism information content (PIC) values among the six duck populations was 0.6269. &nbsp;In most of the duck populations, the mean PIC value was more than 0.5 except in Assam (0.4815) and White Pekin (0.3725) ducks. The observed heterozygosity was the highest in Keeri ducks (0.5217) and lowest in White Pekin ducks (0.2766), while, the mean expected heterozygosity was the highest in Sanyasi (0.5628) and lowest in White Pekin (0.4038) ducks. The variations in the observed and expected number of alleles, differences in PIC of various microsatellite loci might be attributed to the genetic variability of the duck populations, number and type of microsatellite primers utilised for analysis and the genetic diversity of the duck breeds under study. Higher FST value indicates the substantial degree of breed differentiation among the studied duck populations.</div>

<div>Genetic Diversity of Six Duck Populations in India</div>

Genetic diversity of four quail populations, including Korean quails (maroon quails), Peking white quails, Chinese yellow quails and Chinese black quails, were analyzed by microsatellite markers, aiming to provide scientific basis for new breeds of Chinese black quails for egg production as well as the assessment, protection and utilization of Chinese quail&rsquo;s genetic resources. The results showed that 48 alleles were detected by nine microsatellite markers in the four quail populations, with the mean of 5.33 alleles in each locus. The average effective number of alleles marked by the nine microsatellite markers in Chinese black quails, Peking white quails, Chinese yellow quails and maroon quails were 3.5338, 3.6135, 4.0312 and 3.6508 respectively. The average heterozygosity of the four quail populations were 0.6952, 0.7046, 0.7353 and 0.7096 respectively. The average polymorphic information content of nine microsatellite loci in four quail populations were 0.6204, 0.6587, 0.6942 and 0.6639 , respectively, all of which were greater than 0.5, indicating the four populations&rsquo; copious genetic diversity. In this study, the average genetic differentiation coefficient among populations was 0.0349, so the genetic variation among populations accounted for 3.49%, which demonstrated that genetic variation among populations was just a small proportion of the total population genetic variation, and there was little differentiation among the four populations. Cluster analysis indicated that Chinese black quails and Peking white quails were firstly clustered, and then Chinese yellow quails and maroon quails were clustered, and finally the two were clustered together.&nbsp;

Analysis of genetic diversity of four quails by microsatellite markers

<div style="text-align: justify;">An experiment was carried out with 17 CGMS lines and their maintainers along with 22 diversified restorer (R) lines to obtain information on molecular diversity and phenotypic characterization. All exhibited enormous phenotypic variability. Anthocynin pigmentation on hypocotyls was present in 50 genotypes and it was absent in six genotypes viz., ICPA 2043, ICPB 2043, GT 307A, GT 307B, RAJA &amp; BSMR 736. Determinate type of growth habit was found in three genotypes viz., ICPA 2078, ICPB 2078 &amp; GC 11-39. A total of 30 SSR markers were used across 56 genotypes. The polymorphic markers amplified a total of 76 alleles with an average of 2.93 alleles per markers and number of alleles ranged from 2 to 4 per marker. Major allele frequency ranged from 0.34 (CcM0057) to 0.79 (CcM0402) with an average of 0.47 per marker. Molecular diversity among 17 male sterile (A) lines and their maintainer (B) lines yielded three main clusters. All the &lsquo;A&rsquo; and &lsquo;B&rsquo; lines found isogenic, as indicated by close clusters, except for the genotypes GRGA/B 2, GRGA/B 4, GRGA/B 6 and GT 307A/B. Hence more number of back crosses are needed to make them as isonuclear lines.&nbsp;</div>

Molecular diversity and phenotypic characterization of A, B and R lines in Pigeonpea [Cajanus cajan (L.) Millsp.]

Yellow mosaic virus disease is one of the major diseases of soybean in India. Genetic basis of 41 soybean genotypes varying in resistance against yellow mosaic virus was studied using 58 simple sequence repeat primers. A total of 140 alleles with an average of 2.41 alleles per locus were detected, which indicated very narrow genetic base of the genotypes studied. The polymorphic information content varied from 0.00 to 0.754 with an average of 0.357. Unweighted Pair Group Method with Arithmetic Average allocated the genotypes in 2 major clusters separated at 41% similarity with fairly good bootstrap support. Ten unique alleles observed in the study can be used for identification of genotype possessing that particular unique allele. The resistant group comprised of 21 genotypes with similarity coefficient 0.33 to 0.805, of which 20 genotypes were classified in a single sub-cluster. The results presented are of significance with regard to the identification of suitable donor parents for incorporating yellow mosaic resistance into popular soybean varieties. Genetically diverse parents with varying resistance against yellow mosaic virus identified in the study can be used for generating mapping population for the identification of SSR markers closely linked with yellow mosaic virus. &nbsp;&nbsp; &nbsp;

Assessment of genetic diversity of soybean genotypes differing in resistance against yellow mosaic virus using simple sequence repeat markers

Background: The Kachchhi-Sindhi horse is a native Indian breed, mainly found in the Gujarat and Rajasthan regions of India, with an estimated population of about 4,000 horses. A comprehensive genetic assessment to understand the genetic diversity and population structure of this breed is essential for conservation strategies and for maintaining the health and vitality of the breed. 
&nbsp; 
Methods: To determine the genetic diversity and population structure of the Kachchhi-Sindhi breed, we genotyped 50 unrelated, healthy adult horses using 30 microsatellite DNA loci. The genetic data were analyzed to calculate the number of alleles, observed and expected heterozygosity&nbsp; and the inbreeding coefficient (FIS). We also tested for Hardy-Weinberg equilibrium deviations and marker neutrality. We used Structure analysis to assess the admixture within the breed. Besides, population structure analysis was done with principal coordinates analysis (PCoA). Alongside mode shift tests, as well as Sign, Standardized differences and Wilcoxon sign rank tests, were made for assessing signs of a potential population bottleneck recently. 
&nbsp; 
Result: Our study disclosed substantial genetic diversity in the Kachchhi-Sindhi breed. Key genetic parameters averaged an average number of alleles of 10.10&plusmn;3.18, with an effective number of alleles of 5.15&plusmn;1.88 and observed heterozygosity of 0.90&plusmn;0.11, indicating significant genetic variation in the population. The inbreeding coefficient (FIS) was very low at -0.17&plusmn;0.19, indicating limited inbreeding. While 14 of the 30 microsatellites showed deviations from Hardy-Weinberg equilibrium, most markers were considered neutral, with only four showing non-neutral behaviour, according to the Ewens-Watterson neutrality test. Population analysis by PCoA revealed a single large but fragmented population of Kachchhi-Sindhi horses. Further tests, such as the mode-shift test and M ratio value, showed no evidence of a recent bottleneck in the breed. These are crucial for guiding future breeding and conservation efforts for the Kachchhi-Sindhi breed. 
&nbsp;

Genetic Diversity Analysis of Kachchhi-Sindhi Horses and Repercussions for Conservation in India

Genetic diversity among 30 chickpea genotypes was evaluated using simple sequence repeat (SSR) molecular markers. The studies using Sequence Tagged Microsatellite Site (STMS) markers markers revealed that among the primers used across the genotypes produced a total of 35 alleles representing 21 SSR loci with frequencies ranging from one to two (mean 1.66) alleles per locus. Polymorphic Information Content (PIC) ranged from 0.098 to 0.500 (CAM0443, CAM0446). These primers might be an effective and useful tool to determine the genetic differences among chickpea genotypes and to study the phylogenetic relationships. Polymorphic percentage was 96.42. Hierarchical neighbour-joining UPGMA cluster analysis based on simple matching similarity matrix resolved the 30 genotypes into seven clusters. Based on STMS markers highest similarity index 0.850 was observed between BGD 72 and Annigeri-1whereas BGD 9920 and ICC 92944 showed the lowest similarity index 0.214 between them. The STMS clustering pattern indicated the presence of wide genetic diversity between the genotypes. Overall, the study ascertained that SSRs provide powerful marker tools in revealing genetic diversity and relationships in chickpeas, thereby proving useful for selection of parents in breeding programs and also for DNA fingerprinting for identification of cultivars.

Genetic diversity analysis among selected short duration chickpea&nbsp;cultivars and breeding lines based on STMS markers

<div style="text-align: justify;">This study aimed to understand the genetic diversity and population structure of alfalfa germplasm from the United States. In this study, the population structure and genetic diversity of six alfalfa cultivars of United States origin were investigated by microsatellite analysis with 40 individuals per cultivar. A total of 312 discernible alleles were amplified from the whole genome with an average of 31.2 alleles per locus. The average values of polymorphic information content and Shannon&rsquo;s information index were 0.928 and 0.133, respectively, showing high levels of genetic diversity. Two populations were identified by STRUCTURE software with principal coordinate analysis and neighbour-joining clustering. Analysis of molecular variance analysis (AMOVA) revealed that the majority of genetic variation was within cultivars (96.42%) rather than between cultivars (3.58%). In conclusion, analyses of genetic diversity and population structure may be useful for the genetic analysis and utilization of genetic variation in alfalfa breeding.</div>

<div style="text-align: justify;">Genetic diversity studies of alfalfa germplasm (Medicago sativa L. subsp. sativa) of United States origin using microsatellite analysis</div>

<div>Background: Greengram is the fourth dominant pulse crop grown in India and is highly susceptible to bruchids and yellow mosaic virus. Ricebean belonging to the tertiary genepool of greengram shows resistance to this pest and disease. Ricebean being a minor pulse crop has limited SSR markers. Hence, the present study was conducted to test the cross-species amplification of SSR markers derived from related species which could be helpful in studying the molecular diversity available in each crop and for molecular confirmation of the inter- and intra-specific hybrid developed from the crosses. 
 
Methods: Molecular diversity analysis was carried out using 30 genotypes belonging to two species of Vigna (V. radiata and V. umbellata) based on 20 SSR primers derived from adzukibean, commonbean and greengram.&nbsp; 
 
Result: Cross species amplification was observed for all the SSR primers pairs used. The number of alleles detected varied from one (VJ 31122A) to four (CEDAAG 001 and MB 91) with an average of 2.55 alleles per primer. Allele size varied from 100 to 292 bp. The PIC value ranged from zero to 0.611 with an average value of 0.377. Dendrograms constructed based on UPGMA and Neighbour-Joining tree method, grouped the genotypes into five clusters and five groups, respectively. The V. umbellata genotypes were grouped in separate cluster from the V. radiata genotypes in both the methods. The obtained DNA polymorphism at intra- and inter-specific level will facilitate the application of molecular breeding approaches for greengram improvement.&nbsp;</div>

<div>Cross-species Amplification and Molecular Diversity Analysis in Greengram [Vigna radiata (L.) Wilczek] and Ricebean [Vigna umbellata Thunb.]</div>