Mean Number Of Alleles Research Articles

Genetic Diversity of Philippine Native Pigs (Sus scrofa L.) from Quezon and Marinduque Based on Morphological and Microsatellite Markers

Nine microsatellite markers recommended by the Food and Agriculture Organization were used to measure the genetic diversity of Quezon and Marinduque native pig populations – with a total of 37 and 40 individuals, respectively. All markers were discovered to be polymorphic, with a mean number of alleles per locus of 10. Marinduque native pigs were found to have a mean effective number of alleles (EA), mean observed heterozygosity (HO), mean expected heterozygosity (HE), and mean polymorphic information content (PIC) of 5.005 ± 0.547, 0.673 ± 0.040, 0.780 ± 0.024, and 0.76 ± 0.03, respectively. By contrast, Quezon native pigs had mean EA, mean HO, mean HE, and mean PIC values of 5.280 ± 0.787, 0.634 ± 0.044, 0.773 ± 0.035, and 0.75 ± 0.04, respectively. Between the two populations, the heterozygosity (HE > HO) and positive values of FIS (0.1714) and FIT (0.1868) indicated a low number of heterozygotes, suggesting the possibility of inbreeding. The test of Hardy-Weinberg equilibrium (HWE) showed that three loci each in the Quezon and Marinduque native pig populations deviated from HWE. Although morphological analysis revealed significant differences in snout shape, head profile, ear type, and all morphometric traits, a low level of genetic differentiation between the two populations was observed (FST = 0.0186; Nei genetic distance = 0.130; Nei unbiased genetic distance = 0.082). Overall, these findings imply that further studies on the genetic improvement and conservation of Philippine native pigs are required for the development of signature pig breeds across the country.

Genetic Diversity and Structure of the Main Danubian Horse Paternal Genealogical Lineages Based on Microsatellite Genotyping

Simple SummaryThe Danubian horse was created on the former Klementina stud farm near Pleven to satisfy the demands of the Bulgarian Army for light draft horses and to improve the working capacity of the local horse population. The privatization of the Klementina stud farm in the late 1990s and the lack of economic activity have led to a sharp reduction in the number of mares and stallions and their sale to private owners. At present, only six of the main paternal lines which participated in the creation of the Danubian horse breed are preserved: Zdravko, NONIUS XVII-30, Torpedo, Lider, Kalifa, and Hrabar. This is the first study on the genetic and population diversity of the Danubian horse paternal lines based on microsatellite markers (STRs). The results showed that the studied Danubian horse population was characterized by a high level of genetic diversity with a medium value of 0.84. The fixation index (FST) was 0.08 for all studied markers, which is indicative of the low genetic differentiation of the Danubian horse population. Our analysis also confirmed the low level of inbreeding and heterozygous deficiency among the animals selected from the six paternal lineages of the Danubian horse. The present research could be helpful for the development of breeding and conservation programs for the Danubian horse, as well as for making informed decisions on the management of paternal lines.The Danubian horse, together with the Pleven and the Eastern Bulgarian horse breeds, is one of the modern breeds in Bulgaria. The objective of this study was to compare the genetic structure and genetic diversity of six paternal genealogical lineages of the Danubian horse breed (Zdravko, NONIUS XVII-30, Torpedo, Lider, Kalifa, and Hrabar). In total, 166 individuals from the six genealogical lines were investigated, based on 15 STR markers (short tandem repeats, also known as microsatellites). In total, 184 alleles were found in the six populations, using 15 microsatellite loci. The mean number of alleles, the effective number of alleles, and the polymorphic information content (PIC) values per locus were 12.28, 9.48, and 0.73, respectively. In a comparison of the allelic diversity among sire lineages, the highest genetic diversity (Na) was observed in Lider and Kalifa (14.60 ± 0.21), while the lowest value of this parameter was observed in the Zdravko lineage 4.20 ± 0.35. The largest genetic diversity was found in loci HMS3 and HMS7, with 13 alleles, and the smallest polymorphism was noted for the locus ASB17, with 10 alleles. The level of observed heterozygosity was in the range of 0.65 ± 0.069 for the Zdravko lineage to 0.93 ± 0.01 for the Torpedo lineage. The expected heterozygosity level range was from 0.57 ± 0.048 to 0.91 ± 0.01 for all horse lineages. Structure analysis revealed three main gene pools in the study population. The first pool included the Zdravko lineage; the second had the NONIUS XVII-30, Torpedo, Lider, and Kalifa lineages; and the third defined the Hrabar lineage, which was significantly differentiated from the other genealogical lineages.

Analysis of Genetic Diversity in Wild and Domesticated Stocks of the Tropical Abalone Haliotis asinina by Microsatellite Polymorphism

The basic information on genetic diversity of wild and hatchery-propagated stocks of tropical abalone, Haliotis asinina is important for the construction of a breeding scheme leading to the sustainable culturing activity of this species. In this study, 2,876 expressed sequence tags (ESTs) were in silico analyzed and 178 EST sequences contained microsatellite motifs. Four loci (DW455, DW503, PHe177, and PT102) of type I and two loci (Haμ9 and Haμ10) of type II microsatellites were applied for genetic diversity studies. The mean number of alleles per locus and observed heterogeneity in wild populations were 4.167 and 0.483, and 4.833 and 0.528 for CAME (east coast) and TRGW (west coast) while those of hatchery-propagated samples were 3.000 and 0.708, 4.500 and 0.479, 5.167 and 0.524, and 6.333 and 0.527 for PHIH (2nd generation, G2; Philippines), SAMH (G1), SMaRT-TRGH (G8) and SMaRT-SICH (G8), respectively. The numbers of alleles, observed heterozygosity and effective population sizes suggested no severe reduction of genetic diversity in our breeding program of H. asinina. However, reduced Ne was observed in the cultured stocks from the Philippines (PHIH). FST-statistics and the exact test between pairs of samples revealed significant genetic differences between all pairwise comparisons of samples in this study.

Investigation of the genetic structure of some common bean (Phaseolus vulgaris L.) commercial varieties and genotypes used as a genitor with SSR and SNP markers

Common bean is a species belonging to the Phaseolus genus of the Leguminosae family. It has economic importance due to being rich in protein, vitamin A and C, and minerals. Being one of the most cultivated species of legumes, the determination of genetic diversity in bean genotypes or populations has an important role in terms of our genetic resources. The objective of this study was to evaluate the genetic structure of 94 genotypes which were cultivated in different parts of the world and our country with SSR and SNP markers. 10 SSR loci and 73 SNP primers were used for the determination of genetic structure in commercial cultivars and breeding lines. All of the SSR and SNP loci used in the study were found to be polymorphic. A total of 89 alleles were identified for 10 SSR loci. Mean number of alleles per locus (Na = 8.9), effective allele number (Ne = 3.731), Shannon information index (I = 1.468), observed heterozygosity (Ho = 0.023), and expected heterozygosity (He = 0.654) were calculated based on SSR analysis. According to the results of Bayesian-based STRUCTURE analysis using SSR and SNP data, 94 bean genotypes were genetically divided into three main clusters. According to genetic distance based UPGMA dendrogram obtained from SNP analysis, 94 bean genotypes were divided into 2 main clusters corresponding Mesoamerican and Andean gene pools. The obtained results provide important information about the genetic structures of the studied bean cultivars and breeding lines. With the obtained results, it will be possible to develop breeding programs to develop new cultivars by using our gene resources.

Diallel Cross Application and Histomolecular Characterization: An Attempt to Develop Reference Stock of Labeo ariza.

Simple SummaryDiallel crosses are breeding schemes used to estimate combining ability and the effects of reciprocal crosses among strains or varieties. Using this diallel cross scheme, we produced a crossbred population of Ariza labeo (Labeo ariza), a newly potential aquaculture species in Bangladesh. The improved performances of this crossbreed were observed phenotypically (growth performances) and genetically (variation at selected microsatellite loci) and manifested through myofiber histology. Captive breeding of this species in carp hatcheries of Bangladesh could be initiated and facilitated through maintaining the gene pool of the L. ariza of Kangsha and the Atrai River. Conservation could also be considered for advancing the better performer crossbred (G4K♀A♂) as the reference diallel crossbred. The simple yet efficient breeding technique and the manifestation of growth performances using histological and phenotypical observations will encourage the hatchery operators of Bangladesh and elsewhere to initiate the induced breeding of L ariza in large scale aquaculture.The objective of the present study was to evaluate the growth performance and genetic variation in diallel crosses of Ariza labeo (Labeo ariza) originating from three geographically separated rivers (Atrai, Jamuna and Kangsha) in Bangladesh. Intra (G1K♀K♂, G2J♀J♂, and G3A♀A♂) and inter (G4K♀A♂, G5K♀J♂, G6A♀K♂, G7A♀J♂, G8J♀K♂, and G9J♀A♂) stocks were produced following diallel cross (sex ratio—1:1 and n = 48; 16 from each river). Reproductive and growth performance, muscle cellularity and genetic variation following genotyping of eight microsatellite markers (Lr1, Lr2, Lr3, Lr22, Lr24, Lr27, Lr28 and Lr29) and analysis of all crossbreeds was performed. The fertilization (95% ± 2.11%), hatching (88% ± 1.03%), and survival rates (82% ± 1.88%) of G4K♀A♂ were higher compared to other groups. With respect to length and weight gains (2.67 ± 0.4 cm and 3.39 ± 0.2 g), SGR (3.23% ± 0.20%), and heterosis (8.87% and 24.74%) G4K♀A♂ was the superior group. A higher number of hyperplastic muscle fibers, mean number of alleles (2.75) and mean observed heterozygosity (0.417) from G4K♀A♂ could be interpreted to mean that G4K♀A♂ comprise better performance efficiency compared to others and are considered for continuing the L. ariza stock improvement program.

Morphological and molecular characterization of some pumpkin (Cucurbita pepo L.) genotypes collected from Erzincan province of Turkey

Plant genetic resources constitute the most valuable assets of countries. It is of great importance to determine the genetic variation among these resources and to use the data in breeding studies. To determine the genetic diversity among genotypes of Cucurbita pepo L. species of pumpkin, which is widely grown in Erzincan, 29 different pumpkin genotypes collected were examined based on the morphological parameters and molecular characteristics. SSR (Simple Sequence Repeat) markers were used to determine genetic diversity at the molecular level. The analysis of morphological characterization within genotypes showed a wide variability in morphological traits of plant, flower, fruit, and leaf. In the evaluation performed using SSR markers, all primers exhibited polymorphism rate of %100. Seven SSR markers yielded a total of 15 polymorphic bands, the number of alleles per marker ranged from 2 to 3, and the mean number of alleles was 2.14. Polymorphic information content (PIC) ranged from 0.06 (GMT-M61) to 0.247 (GMT-P41), and the mean PIC value per marker was 0.152. Cluster analysis using Nei's genetic distance determined that 29 genotypes were divided into 4 major groups. The present findings have revealed the genetic diversity among pumpkin genotypes collected from Erzincan province and may form the basis for further breeding studies in pumpkin.

Genetic and Population Structure of Croatian Local Donkey Breeds

The two native Croatian donkey breeds (Littoral-Dinaric donkey and Istrian donkey) were marginalized in the second half of the 20th century and were on the verge of biological extinction. The aim of this study was to analyze the demographic and genetic status of two donkey breeds, two decades after the start of protection by analyzing their pedigrees and genetic structure. The average generation interval was higher for the Istrian donkey (7.73) than for the Littoral-Dinaric donkey (7.27). The rate of the effective number of founders compared with the effective number of ancestors in the Littoral-Dinaric donkey (1.03; 325/316) and in the Istrian donkey (1.08; 70/65) revealed no evidence of a genetic bottleneck. The inbreeding coefficient (F) and the average relatedness coefficient (AR) was lower in the Littoral-Dinaric donkey population (0.99%; 0.13%) than in the Istrian donkey population (1.77%; 1.10%). Genetic microsatellite analysis showed relatively high genetic diversity in Littoral-Dinaric donkey and Istrian donkey breeds, expressed by mean allele number (5.92; 5.85) and expected heterozygosity (0.650; 0.653). Genetic differentiation between the Littoral-Dinaric donkey and the Istrian donkey has not significantly increased in the last two decades (FST = 0.028). Genetic analysis also showed no evidence of high inbreeding or genetic bottleneck in both breeds. A total of 11 haplotypes including 28 polymorphic sites were found in 30 samples. Analysis of mtDNA has shown that the Littoral-Dinaric donkey and Istrian donkey breeds belong to the Equus asinus africanus group. The study confirms the need to use different analytical approaches to get a regular and complete insight into the situation and trends within and between breeds, so that the existing diversity can be fully preserved.

Genetic diversity of Greek grapevine (Vitis viniferaL.) cultivars using ampelographic and microsatellite markers

AbstractGrapevine (Vitis viniferaL.) is a major worldwide crop of high economic importance, tightly interwoven with the traditions and the culture of many civilizations. The Greek vineyard is one of the oldest in the world composed of an ample number of highly diverse indigenous landraces. However, over the last decades the local cultivated grapevine germplasm has undergone a drastic reduction of diversity, due to the established market preferences for international varieties. In the current work a combined approach involving both, ampelographic traits and microsatellite markers has been undertaken, to study the genetic diversity within and among 96 grapevine genotypes belonging to 36V. viniferasubsp.viniferacultivars, predominantly representing autochthonous Greek landraces. Results revealed high genetic diversity for the Greek cultivars yielding a mean number of alleles per locus 14.69 and mean polymorphic information content 0.848. Hierarchical cluster analysis, employing both, ampelographic and microsatellite data, showed a clear distinction based on the origin of the germplasm; Anatolian versus Mediterranean. Principal component analysis, based on the most informative ampelographic traits, coupled to the results from genetic structure analysis further corroborated the proposal of germplasm differentiation on the basis of geographic origin. This information can be further utilized for the reconstitution of the Greek vineyard and can significantly contribute towards a rational conservation and utilization strategy for breeding or for direct cultivation of the Greek indigenous grapevine germplasm.

Turkish durum wheat conserved ex‐situ and in situ unveils a new hotspot of unexplored genetic diversity

AbstractDurum wheat (Triticum turgidum L.) is the 10th most cultivated crop and is a vital food source for human consumption. Genetic diversity in durum wheat is still an unexplored subject, and gene banks are filled with accessions waiting to be screened. Here, four different groups of durum wheat, Turkish and foreign cultivars, and in situ and ex situ landraces were evaluated for population structure and genetic diversity. A collection of 129 durum wheat accessions were genotyped, with a total of 6,357 markers (SilicoDArT, SNP [single‐nucleotide polymorphism], and simple sequence repeats [SSRs]). The highest mean allele number per marker (1.562) was obtained with SNP markers in ex situ landraces; the lowest mean allele number per marker (0.788) was obtained with SSR markers in the foreign cultivars. The minimum percentage of polymorphic loci was 38.70% observed with SSR markers in foreign cultivars; the maximum was 76.20% in SilicoDArT markers in ex situ landraces. According to Neighbor‐Joining analyses, the studied collection was divided into groups of cultivars and landraces, with some level of admixtures. Structure and principal coordinate analysis obtained distinct clusters for ex situ landraces and foreign cultivars, supported by Neighbor‐Joining analysis. A significant level of intergroup and intragroup variation was observed, and Turkish ex situ landraces were found as the most diverse and distinct group in the collection. Turkish landraces may be a promising source of novel allelic diversity that can be used in durum wheat breeding worldwide.

Microsatellite Genotyping of Two Bulgarian Sheep Breeds

The aim of this study was to compare the genetic structure and genetic diversity of two Bulgarian sheep breeds. A total of 41 individuals from a modern Bulgarian sheep population (Rhodopean Tsigai, RT) and 46 representatives of a local Bulgarian sheep population (Middle Rhodopean Sheep, MRS) were investigated based on 12 STR (short tandem repeat, also known as microsatellite) markers. In total, 121 alleles were found in the two populations using 12 microsatellite loci. The mean number of alleles, the effective number of alleles, and the polymorphism information content (PIC) values per loci were 10.08, 4.96, and 0.73, respectively. When comparing the allelic diversity across the populations, the highest Na was observed in the MRS breed (10.58 ± 0.87), while the value of this parameter in the RT breed was 9.58 ± 0.71. The largest genetic diversity was found at locus INRA005 with 14.5 alleles and the smallest polymorphism was noted for locus ETH152 with 5.5 alleles. The level of observed heterozygosity was in the range of 0.60 to 0.860. The expected heterozygosity level range was 0.62 to 0.87. When 12 microsatellite loci were compared, the INRA005 locus showed the highest level of genetic variability. Using Nei’s standard genetic distance, the observed genetic distance between the RT and MRS breeds was 0.103. Both sheep breeds demonstrated mixed genetic profiles based on the studied microsatellite markers. The clustering obtained by STRUCTURE analysis showed that the MRS breed is a more homogenous population, whereas the RT breed is more heterogenous.

Genetic diversity and population structure of four Nigerian indigenous cattle breeds.

A total of thirty-eight (38) Nigerian indigenous cattle were used to evaluate the genetic relatedness, diversity, and population structure of four indigenous cattle breeds. Blood samples were collected from the experimental animals into vacutainer tubes containing EDTA, and genomic DNA extracted, quantified, and evaluated for integrity. Fourteen (14) microsatellite primers were used for polymerase chain reaction (PCR) and PCR amplification performed under standard conditions followed by electrophoresis in 2.5% Metaphor Agarose gel. Genomic parameter estimates included allele number (Na), observed (Ho) and expected (He) heterozygosity, polymorphism information content (PIC), test of Hardy-Weinberg equilibrium, and genetic diversity; pairwise Nei's genetic distance, Wright's F-statistics (FIT, FST, and FIS), and gene flow (Nm); and breed relationship, population structure, and degree of admixture. A total of 112 alleles were detected and mean number of alleles was 4.02 ± 0.190, while mean fixation index was 0.461 ± 0.068. Mean Ho and He were 0.352 ± 0.05 and 0.605 ± 0.018, respectively. Pairwise estimates of genetic differentiation, FST, were significantly different (p < 0.001) implying distinct breeds. Estimates of Nm were less than 4 but greater than 1, indicating that the cattle breeds do not belong to one panmictic population. Estimates of pairwise genetic distance revealed that White Fulani and Sokoto Gudali were more closely related than Muturu and N'Dama. The results of STRUCTURE, principal coordinate, and phylogenetic analyses revealed four clusters which implies that the breeds were genetically distinct. It is recommended that the four cattle breeds can be used to develop composites with higher genetic potentials for beef production and resistance to endemic diseases and pests. Further efforts should be made to conserve and genetically improve these breeds to meet present and future production and breeding imperatives.

Genetic Diversity and Structure in a Closed Breeding System of Russian Honey Bees.

High levels of genetic diversity are critical to the success of breeding programs. Russian honey bees are a selected stock that undergoes breeding in a closed block-based mating system. Given its established history, Russian stock has longitudinal measures of genetic integrity (i.e., genetically based stock identity) and diversity. Assessments using genetic stock identification (GSI) have shown that genetic diversity parameters were assessed across breeding blocks for three generations, spanning 6 yr (2014, 2017, and 2020), showing levels comparable to those when the stock was initially released in 2008. Allelic richness (mean number of alleles) and gene diversity levels were consistent over time and among blocks. Blocks were generally not differentiated from one another within each year. However, the 2020 population was distinct when compared with bees sampled in both 2014 and 2017. Genetic distance relationships supported differentiation of the 2020 population by distinct clustering. The patterns observed here are consistent with historical changes made to the breeding program to increase stringency of the selection criteria.

Structure and genetic diversity of two populations of Garcinia kola Heckel (Clusiaceae) revealed by RAPD markers

This study aims to characterize the genetic diversity of two populations of Garcinia kola using five RAPD markers in order to contribute to the development of sustainable management and conservation strategy for this species. Genomic Deoxyribonucleic acid (DNA) extracted from leaf fragments of 94 trees from two agroecological (south and west) zones according to Cethyl Trimethyl Ammonium Bromide (CTAB) protocol was analyzed. The mean number of alleles was ranged from 14.2 to 21.2 and the effective number of alleles ranged from 8.62 to 9.44. The average Shannon diversity index was ranged from 2.08 to 2.59 and the average genetic diversity was estimated to be 0.80. A total of 58 polymorphic bands were identified with a polymorphism rate of 100%. According to analysis of molecular variance the most important component of the genetic variation was obtained within population (94%). The analysis of the genetic diversity of all the trees revealed the existence of two groups composed of the trees from the two populations. In addition, genetic differentiation between the two populations was relatively moderate (Fst = 0.061). Sustainable management of G. kola trees should be achieved through in situ conservation. But for ex situ conservation it would be more practical to take as many individuals as possible within populations.

The genetic diversity of safflower (Carthamus tinctorius L.) genotypes developed by hybridization using SSR markers

Safflower is an annual oilseed crop which has healthy edible oil containing high amount of unsaturated fatty acids in the world. In this study, we investigated safflower registered cultivars of Turkey (4), genotypes retrieved from USDA (10) and their hybrids (45) for genetic variation using 10 simple sequence repeat (SSR) loci. Genetic diversity calculated registered cultivars, genotypes and hybrids were as follows: mean number of alleles (4.67), expected heterozygosity (0.680), average effective number of alleles (3.172), and polymorphism information content (0.664). The dendrogram analysis revealed at least four possible major clusters in the parents and hybrids. High level of genetic diversity explained between the populations and Fst calculate (0.593) suggested that the clusters were differentiated to each other. Registered safflower cultivars of Turkey were distributed across all four clusters and the accessions from USA were defined in most of the clusters. The dendrogram based method analysis revealed two major clusters which corresponded to spiny and spineless safflower genotypes. It was suggested that the studied 6 SSR markers could be utilized for safflower breeding studies based on molecular analysis.

Investigating population dynamics from parentage analysis in the highly endangered fan mussel Pinna nobilis.

Understanding dispersal patterns is a major focus for conservation biology as it influences local survival and resilience in case of local disturbance, particularly for sessile species. Dispersal can be assessed through parentage analyses by estimating family structure and self‐recruitment. This study documents the family structure of a pelagic spawner, Pinna nobilis, which is facing a major crisis that threatens its survival as most of its populations have been decimated by a parasite, Haplosporidium pinnae. In this context, we focused on a single population (Peyrefite, Banyuls‐sur‐mer, France) where 640 individuals were sampled in 2011, 2015, and 2018 and genotyped for 22 microsatellite markers. Genetic diversity was high and homogeneous among years, with mean allele numbers ranging between 13.6 and 14.8 and observed heterozygosities (H o) between 0.7121 and 0.7331. Low, but significant, genetic differentiations were found between 2011–2015 and 2015–2018. A parentage analysis described 11 clusters, including one prevailing, and revealed that 46.9% of individuals were involved in half‐sib relationships, even between years, suggesting that source populations were recurrent year after year. There were few individuals resampled between years (30 in 2015 and 14 in 2018), indicating a rapid turnover. Considering the large number of half‐sib relationships but the low number of relations per individual, we conclude that P. nobilis exhibit homogeneous reproductive success. Self‐recruitment was not detected, making this population highly vulnerable as replenishment only relies on connectivity from neighboring populations. In the context of the pandemic caused by H. pinnae, these results will have to be considered when choosing a location to reintroduce individuals in potential future rescue plans.

Characteristics of the Allele Pool and the Genetic Differentiation of Goats of Different Breeds and their Wild Relatives by Str-Markers.

Based on 16 STR-loci, the allele pool and interbreed differentiation of goat breeds of Russian and foreign breeding were investigated in this study. These breeds included Karachai (KRCH-K, n=73, mountain zone; KRCH-Z, n=33, foothill zone), Dagestan Downy (DAGD, n=30), Dagestan Wool (DAGW, n=30), Soviet Wool (SOVW, n=30), Saanen (SAAN, n=34), Murciano-Granadina (MURS, n=37), as well as wild goats, represented by three species of mountain goats (n=52): Siberian Capricorn (Capra sibirica) of Altai (CSIB-S, n=6), Tajikistan (CSIB-T, n=4), Kyrgyzstan (CSIB-K, n=6), and the Himalayas (CSIB-H, n=4); Bezoar goat (Capa aegagrus) of Turkey (CAEG, n=3) and Pakistan (CAEG-S, n=3); West Caucasian tur (Capra caucasica): western Caucasian (Kuban, CCAU-K, n=10), central Caucasian (CCAU-M, n=8), and eastern Caucasian (Dagestan, CCAU-D, n=8). The highest genetic diversity was observed in the North Caucasus breeds, such as Karachai, Dagestan Downy, and Dagestan Wool. The mean numbers of alleles per locus and allelic diversity were 7.385-9.154 and 7.353-7.713, respectively. The genetic proximity of Caucasian breeds was confirmed by cluster analysis, and they formed a common branch with the highest genetic affinity, while the Orenburg and Soviet Wool breeds formed another branch, and the third branch with the least affinity was the dairy breed of foreign selection.The analysis of the phylogenetic tree of domestic and wild species established the formation of three clusters formed by the subspecies of the West Caucasian tur, Siberian ibex, and breeds of domestic goats. At the same time, populations of the Bezoar goats were localized at the root of the last cluster, which confirmed their role as the ancestors of domestic goats.

High Genetic Diversity but Absence of Population Structure in Local Chickens of Sri Lanka Inferred by Microsatellite Markers.

Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (FIS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative FIS were observed. The positive FIS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.

Morpho-molecular characterization and genetic diversity analysis across wild apple (Malus baccata) accessions using simple sequence repeat markers

Out of five wild Malus species in the world, Malus baccata (L.) Borkh (MB) is reported from the extremely cold areas of north western Himalayas. These are widely used as a rootstock or source of resistance against various biotic and abiotic stresses due to its ecological adaptability and cold hardiness. The study of genetic diversity is an important aspect to be covered for proper utilization of the wild apple germplasm for breeding purpose. The 29 Malus baccata accessions were used to divulge their genetic diversity using morpho-molecular markers. Based on morphological characters, Mahalanobis D2statistics resolved all accessions in four clusters. A set of 85 SSR were used to study molecular diversity among the accessions. The AMOVA stated genetic diversity between populations of genotypes was lower (7%) compared to that observed within and among the individuals of the populations (93%). The effective allele number (2.63) was found to be lower than mean allele number (3.7), with mean heterozygosity as 0.51. The gene diversity varied between 0.10 for Hi02d05 to 0.79 for CH-Vf1.The expected heterozygosity was greater than observed heterozygosity for total analysed loci of SSR. The average PIC value was found as 0.50. The accessions were segregated into two distinct classes using heirarchical clustering method. Further, population structure also differentiated the 29 accessions into two populations, with sub-population I accounts for 18 accessions and sub-population II consisted of only 9 accessions. MB-5 and MB-20 accessions fall in the admixture group. The differentiated populations were validated and reconfirmed by the PCoA analysis. . The morphological features and molecular markers revealed significant level of genetic diversity along with population differentiation among the maintained accessions.

Dissection of Allelic Variation Underlying Floral and Fruit Traits in Flare Tree Peony (Paeonia rockii) Using Association Mapping.

Allelic variation in floral quantitative traits, including the elements of flowers and fruits, is caused by extremely complex regulatory processes. In the genetic improvement of flare tree peony (Paeonia rockii), a unique ornamental and edible oil woody species in the genus Paeonia, a better understanding of the genetic composition of these complex traits related to flowers and fruits is needed. Therefore, we investigated the genetic diversity and population structure of 160 P. rockii accessions and conducted single-marker association analysis for 19 quantitative flower and fruit traits using 81 EST-SSR markers. The results showed that the population had a high phenotypic diversity (coefficients of variation, 11.87–110.64%) and a high level of genetic diversity (mean number of alleles, NA = 6.09). These accessions were divided into three subgroups by STRUCTURE analysis and a neighbor-joining tree. Furthermore, we also found a low level of linkage disequilibrium between these EST-SSRs and, by single-marker association analysis, identified 134 significant associations, including four flower traits with 11 EST-SSRs and 10 fruit traits with 32 EST-SSRs. Finally, based on the sequence alignment of the associated markers, P280, PS2, PS12, PS27, PS118, PS131, and PS145 may be considered potential loci to increase the yield of flare tree peony. These results laid the foundation for further analysis of the genetic structure of some key traits in P. rockii and had an obvious potential application value in marker-assisted selection breeding.

Characterization of a new potential goat breed (Palamu) from Jharkhand, India

Palamu goat forms the part and parcel of the lives of the farmers and tribes of Jharkhand. Palamu goat also known as Medini is named after its distribution area (Palamu, Latehar and Garhwa) in Jharkhand. This small size goat is reared in Jharkhand since time immemorial. Average flock size is 5.36±0.19 and varies from 1 to 31. Twinning is common except in first kidding. Head profile is convex, ears are pendulous, and horns are straight with backward and upward orientation. Muzzle, eyelids and hooves are black, body is cylindrical, udder is small and pendulous and teats are conical shaped. Age at first mating in males is 8.32±0.86 (months) that vary between 7.2– 9.2 months. Corresponding values for female are 7.22±1.35 months varying between 6.7–7.7 months. Diversity status of the population was explored using 25 microsatellite markers. A total of 190 alleles were detected and sufficient polymorphism was evident from the allele frequency data. ILSTS82 showed the highest number of observed alleles per locus (20) while RM4 and ILSTS05 showed the lowest (4) with 9.14±2.0 as mean number of alleles. Expected number of alleles varied from 1.49 (ILSTS065) to 7.55 (ILSTS30) with the mean value of 4.15±0.91. Palamu goat had substantial genetic variation based on its gene diversity in addition to the average number of alleles per locus. The observed and expected heterozygosity values were 0.64±0.14 and 0.69±0.15, respectively. Observed heterozygosity was lower than expected showing a departure from Hardy-Weinberg Equilibrium (HWE) and possibility of inbreeding. Population has heterozygote deficiency to the tune of 9% (FIS value=0.09). Population did not suffer from recent genetic bottleneck (last 40–80 generations). The results suggest existence of a distinct goat population harboring sufficient genetic variation for scientific management.