Microsatellite-based phylogeny of Indian domestic goats

Analysis of the population genetic structure using microsatellite markers in goat populations in Taiwan

Due to the poor growth rate of the Taiwan black (TB) goat in Taiwan, many exotic breeds were brought into breeding schemes to improve TB goat. However, the excessive cross-breeding of alien species with TB goat has decreased its population numbers, genetic variation and biodiversity. Therefore, TB goat population considered an endemic species in Taiwan that needed to be conservation. The objective of the present study was to analyze the genetic structure and TB goat using genetic markers for genetic improvement and to sustain germplasm conservation and utilization. 15 microsatellite markers, divided into three sets, were used to analyze 690 goats sampled from 10 goat populations. The average number of alleles (Na) and effective alleles (Ne) was 11.87 ± 3.93 and 5.093 ± 1.768, respectively. The average expected heterozygosity (HE) and observed heterozygosity (HO) was 0.780 ± 0.084 and 0.602 ± 0.116, respectively. The average polymorphic information content (PIC) was 0.747 ± 0.103; FIS was 0.058 ± 0.075. All 15 microsatellite markers were highly polymorphic. The genetic distances between individuals were estimated to construct a phylogenetic tree. In present study, the 690 goat samples were divided into 8 clusters. The results indicated that these 15 microsatellite markers successfully clustered goat populations in Taiwan and could assist in the preservation of TB goats.

Genetic diversity evaluation of Sojat goat population of India

Sojat goat forms the part and parcel of the lives of the farmers in the Barmer region of Rajasthan. These are large-sized goats, white in colour, and have dual utility. These goats fetch premium price during the Eid festival. Assessment of diversity is essential for germplasm characterization and management. Genomic microsatellite markers being a valuable tool for estimating genetic diversity were selected for exploring existing genetic variability in the Sojat goat population. The standard metrics of genomic diversity detected moderate variability with a total of 162 alleles across 22 loci in this lesser-known population. The expected number of alleles had a mean value of 3.40±0.39. Similarly, a moderate magnitude of diversity was recorded in the Sojat population as the mean observed heterozygosity was 0.54±0.05. Expected heterozygosity was higher than the observed (0.60±0.06), indicating a deviation from Hardy-Weinberg Equilibrium (HWE) and the possibility of inbreeding due to the non-random mating in the population. Accordingly, significant heterozygote deficiency was noticed (F=0.08±0.03). The population did not suffer a reduction in effective population size in the last few generations. Mutation drift equilibrium did not reveal significant heterozygosity excess under different models of microsatellite evolution and no shift was recorded in the frequency distribution of alleles. To conclude, the results provided the first insights into the genetic diversity of Sojat goats. A moderate genetic variability with heterozygote deficiency within the population warrants immediate attention for scientific management of this unique goat population to conserve the existing genetic variation and to avoid any escalation of inbreeding.

Genetic Differentiation among Livestock Breeds—Values for Fst

Simple Summary

The degree of relationship among livestock breeds can be quantified by the F_st statistic, which measures the extent of genetic differentiation between them. An F_st value of 0.1 has often been taken as indicating that two breeds are indeed genetically distinct, but this concept has not been evaluated critically. Here, F_st values have been collated for the six major livestock species: cattle, sheep, goats, pigs, horses, and chickens. These values are remarkably variable both within and between species, demonstrating that F_st > 0.1 is not a reliable criterion for breed distinctiveness. However, the large body of F_st data accumulated in the last 20–30 years represents an untapped database that could contribute to the development of interdisciplinary research involving livestock breeds.

Abstract

(1) Background: The F_st statistic is widely used to characterize between-breed relationships. F_st = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding F_st values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed F_st were as follows, cattle: microsatellite 0.06–0.12, SNP 0.08–0.15; sheep: microsatellite 0.06–0.10, SNP 0.06–0.17; horses: microsatellite 0.04–0.11, SNP 0.08–0.12; goats: microsatellite 0.04–0.14, SNP 0.08–0.16; pigs: microsatellite 0.06–0.27, SNP 0.15–0.22; chickens: microsatellite 0.05–0.28, SNP 0.08–0.26. (4) Conclusions: (1) Large amounts of F_st data are available for a substantial proportion of the world’s livestock breeds, (2) the value for between-breed F_st of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated F_st data may have value for interdisciplinary research.

Aspects of Molecular Genetics in Dromedary Camel

Dromedary camels are unique in their morphological and physiological characteristics and are capable of providing milk and meat even under extreme environmental conditions. Like other species, the dromedary camel has also benefitted from the development of the molecular genetics to increase the knowledge about different aspect in camel genetics (genetic variation, molecular marker, parentage control, gene of interest, whole genome, dating…etc.). In this paper we review the different molecular genetic technics used in this particular species and future prospects. Dromedary genetic studies started in the end of the 1980s with phenotypic evaluation and the attempts to highlight the protein and biochemical diversity. In the 2000s, with the development of molecular markers such as microsatellites, genetic diversity of different types in several countries were estimated and microsatellites were also used for parentage control. In terms of genetic characterization, microsatellites revealed a defined global structure, differentiating East African and South Arabian dromedaries from North African, North Arabian, and South Asian individuals, respectively. Also, mitochondrialDNA sequence analysis of ancient DNA proved to be crucial in resolving domestication processes in dromedaries. Ancient and modern DNA revealed dynamics of domestication and cross-continental dispersion of the dromedary. Nuclear SNPs, single nucleotide polymorphisms changes that occur approximately each 1000 bps in the mammalian genome were also applied in some studies in dromedary. These markers are a very useful alternative to microsatellites and have been employed in some studies on genetic diversity and relevant phenotypic traits in livestock. Finally, thanks to the use of Next Generation Sequencing (NGS) the whole-genome assemblies of the dromedary (Camelus dromedarius) and a work to establish the organization of the dromedary genome at chromosome level were recently published.

Transcriptomic diversity in longissimus thoracis muscles of Barbari and Changthangi goat breeds of India

The present study is an attempt to examine the differential expression of genes in longissimus thoracis muscles between meat and wool type Indian goat breeds. Barbari goat is considered the best meat breed while Changthangi is famous for its fine fibre quality. RNA sequencing data was generated from four biological replicates of longissimus thoracis muscles of Barbari and Changthangi goats. A clear demarcation could be observed between the breeds in terms of expression of genes associated with lipid metabolism (FASN, SCD, THRSP, DGAT2 and FABP3). Most significant genes with high connectivity identified by gene co-expression network analysis were associated with triacylglycerol biosynthesis pathway in Barbari goat. Highly interactive genes identified in Changthangi goat were mainly associated with muscle fibre type. This study provides an insight into the differential expression of genes in longissimus thoracis muscles between Barbari and Changthangi goats that are adapted to and reared in different agro-climatic regions.

Whole genome analysis of Black Bengal goat from Savar Goat Farm, Bangladesh

OBJECTIVES

Single nucleotide polymorphisms (SNPs) play critical roles in genetic diversity and disease. Many traits and diseases are linked with exonic SNPs that are significant for gene function, regulation or translation. This study focuses on SNPs that potentially act as the genetic basis for desirable traits in the Black Bengal Goat. This variety of goat is native to South Asia, and is identified as one of the most commercially important meat producing animals in the world. The aim of this study was to sequence the genome of Black Bengal Goats and identify SNPs that might play a significant role in determining meat quality in the organism. The study focuses on exonic SNPs for their greater likelihood of affecting the final translated protein product.

RESULTS

Approximately 76,000 exonic variants were identified in the study. After filtration using a Wilcoxon test based score, the number came down to 49, 965 which were found to be distributed in 11,568 genes. The functional pathways affected by these variations included fatty acid metabolism and degradation, which are important processes that influence meat quality.

Genetic characterization of Markhoz goat breed using microsatellite markers

The use of molecular markers can support the management of endangered populations and should be combined with appropriate breeding strategies to improve productive traits avoiding the decline of the breed. The genetic variability at 10 microsatellite loci were investigated in a sample of 100 unrelated Markhoz goats (77 females and 23 males). The investigated population was reared at the Sanandaj Markhoz goat Performance Testing Station in Kurdistan, Iran. Markhoz goat, a multipurpose breed, is one of the most valuable genetic resources in Iran. All the studied loci were found to be polymorphic and a total number of 52 alleles were identified with an average number of alleles of 5.2. Moreover, some population genetic indices, such as observed and expected heterozygosity, observed and expected number of alleles, Shannon's index, Nei's expected heterozygosity, and polymorphism information content were also calculated. Despite the decreasing population size, Markhoz goat genetic diversity is still conserved. The breed seems to have a good level of genetic variability and, as a consequence, a potential margin of adaptability to environment and for future genetic improvement.

Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing pieces

Domestic goats (Capra hircus) are spread across the five continents with a census of 1 billion individuals. The worldwide population of goats descends from a limited number of bezoars (Capra aegagrus) domesticated 10 000 YBP (years before the present) in the Fertile Crescent. The extraordinary adaptability and hardiness of goats favoured their rapid spread over the Old World, reaching the Iberian Peninsula and Southern Africa 7000 YBP and 2000 YBP respectively. Molecular studies have revealed one major mitochondrial haplogroup A and five less frequent haplogroups B, C, D, F and G. Moreover, the analysis of autosomal and Y-chromosome markers has evidenced an appreciable geographic differentiation. The implementation of new molecular technologies, such as whole-genome sequencing and genome-wide genotyping, allows for the exploration of caprine diversity at an unprecedented scale, thus providing new insights into the evolutionary history of goats. In spite of a number of pitfalls, the characterization of the functional elements of the goat genome is expected to play a key role in understanding the genetic determination of economically relevant traits. Genomic selection and genome editing also hold great potential, particularly for improving traits that cannot be modified easily by traditional selection.

Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics

The Korean native horse (Jeju horse) is one of the most important animals in Korean historical, cultural, and economical viewpoints. In the early 1980s, the Jeju horse was close to extinction. The aim of this study is to explore the phylogenomics of Korean native horse focusing on spatio-temporal dynamics. We determined complete mitochondrial genome sequences for the first Korean native (n = 6) and additional Mongolian (n = 2) horses. Those sequences were analyzed together with 143 published ones using Bayesian coalescent approach as well as three different phylogenetic analysis methods, Bayesian inference, maximum likelihood, and neighbor-joining methods. The phylogenomic trees revealed that the Korean native horses had multiple origins and clustered together with some horses from four European and one Middle Eastern breeds. Our phylogenomic analyses also supported that there was no apparent association between breed or geographic location and the evolution of global horses. Time of the most recent common ancestor of the Korean native horse was approximately 13,200-63,200 years, which was much younger than 0.696 My of modern horses. Additionally, our results showed that all global horse lineages including Korean native horse existed prior to their domestication events occurred in about 6000-10,000 years ago. This is the first study on phylogenomics of the Korean native horse focusing on spatio-temporal dynamics. Our findings increase our understanding of the domestication history of the Korean native horses, and could provide useful information for horse conservation projects as well as for horse genomics, emergence, and the geographical distribution.

Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach

Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds.

Microsatellite DNA typing for assessment of genetic variability in Marwari breed of Indian goat

Aim:

To estimate existing within-breed genetic variability in Marwari goats under field conditions and the generated data that can be used to determine genetic relationships with other breed of goats.

Materials and Methods:

A total of 146 blood samples of goats of Marwari breed were randomly collected from genetically unrelated animals from different villages of Bikaner Districts of Rajasthan, India. Genomic DNA was extracted from whole blood using proteinase K-digestion followed by standard phenol–chloroform extraction procedure at room temperature and confirmed through horizontal electrophoresis on 0.8% agarose gel containing ethidium bromide. Fifteen caprine microsatellite markers were used to estimate genetic variability among the goats of Marwari breed in terms of allelic and genotype frequencies, heterozygosities and polymorphism information content (PIC) value.

Results:

A total of 74 alleles were contributed by Marwari goat across all 15 microsatellite loci. The number of alleles per locus varied from two (ILSTS-087) to 9 (ILSTS-058) alleles, with a mean of 4.93 whereas the effective number of allele varied from 1.35 (ILSTS-005) to 3.129 (ILSTS011) with a mean of 2.36. The effective number of allele is lesser than observed number at all the loci. Allelic sizes ranged from 125 bp (ILSTS-028 and ILSTS-033) to 650 bp (ILSTS-011 and ILSTS-019). The expected heterozygosity ranged from 0.240 (locus ILSTS-005) to 0.681 (locus ILSTS-011), with an average value of 0.544. The observed heterozygosity (Ho) ranged from 0.1428 (locus ILSTS-087) to 0.9285 (locus ILSTS-034), with an average value of 0.5485 indicates substantial and very good number of heterozygotes, in the population. The highest PIC value (1.1886) was observed at ILSTS-044 locus and least (0.0768) at ILSTS-065 locus for Marwari goat.

Conclusion:

Microsatellite analysis revealed a high level of polymorphism across studied microsatellite markers and informativeness of the markers for genetic diversity analysis studies in Marwari goats. This high level of polymorphism can be utilized to plan future biodiversity studies to exploit the uniqueness and adaptability of this breed to Western Rajasthan. Most studied microsatellite markers proving to be good candidates for genetic characterization and diversity analysis of this breed of goat.

Genetic characterization of Gaddi goat breed of Western Himalayas using microsatellite markers

Aim:

In the present study, genetic characterization of Gaddi goat breed, a native to north temperate western Himalayan region of India, was carried out for the purpose of breed characterization and assessing existing intra-population genetic diversity.

Materials and Methods:

Totally, 75 blood samples procured at random from genetically unrelated animals of two sexes and different age groups and true to breed type were collected from different locations in the breeding tract of these goats in Himachal Pradesh, of which only 51 samples with desired quantity and quality were subjected to further processing for DNA isolation. The multi-locus genotype data were generated on 51 Gaddi goats sampled across different regions of the breeding tract in Himachal Pradesh using 15 FAO recommended goat specific microsatellite markers, which gave amplification and observed and effective number of alleles, gene frequency, observed and expected heterozygosity were estimated through PopGene software (1.3.1).

Results:

A total of 135 distinct alleles were observed with mean observed and effective number of alleles as 9.0000±0.82 and 6.5874±0.56 respectively across all 15 studied loci. The maximum (15) alleles were contributed by loci DRBP1 and P19/DYA and the least (5) by SRCRSP5. The mean heterozygosity was observed to be 0.8347±0.01 ranging from 0.7584 (SRCRSP5) to 0.9156 (P19-DYA) across all loci. The mean observed (H_O) and expected (H_E) heterozygosities across all loci were 0.7484±0.02 and 0.8431±0.01 respectively. The polymorphism information content (PIC) value ranged from 0.7148 (SRCPS5) to 0.909 (P19-DYA) with mean PIC of 0.8105±0.01 in the present study. The average heterozygosity was observed to be 0.8347±0.01 ranging from 0.7584 (SRCRSP5) to 0.9156 P19 (DYA) across all loci.

Conclusion:

Microsatellite analysis revealed high level of polymorphism across studied microsatellite markers and informativeness of the markers for genetic diversity analysis studies in Gaddi goats. This high level of polymorphism can be utilized to plan future association studies to exploit the uniqueness and adaptability of indigenous Gaddi goat breed of Western Himalayas. Most studied microsatellite markers had desired neutrality, thus proving to be good candidates for genetic characterization and diversity analysis in Gaddi breed of goats also.

Genetic diversity and structure in Asian native goat analyzed by newly developed SNP markers

In the current study, a total of 65 single nucleotide polymorphisms (SNPs) within the intron region were developed in goat (Capra hircus) by utilizing genomic information of cattle and sheep due to poor available genomic information on goat. Using these markers, we carried out genetic diversity and structure analyses for 10 Asian goat populations. The phylogenetic tree and principal components analysis showed good correspondence between clustered populations and their geographic locations. The STRUCTURE software analysis illustrated six divergent genetic structures among 10 populations. Myanmar and Cambodia populations showed high admixture patterns with different ancestry, suggesting genetic introgression into native goat populations. We also investigated the correlation between genetic diversity and geographic distance from a domestication center. This result showed a decreasing trend of genetic diversity according to the distance (P = 0.014). This result supported common consensus that western Asia is one of the centers of origin for modern Asian domestic goat.

Genetic diversity and investigation of polledness in divergent goat populations using 52 088 SNPs

The recent availability of a genome-wide SNP array for the goat genome dramatically increases the power to investigate aspects of genetic diversity and to conduct genome-wide association studies in this important domestic species. We collected and analysed genotypes from 52 088 SNPs in Boer, Cashmere and Rangeland goats that had both polled and horned individuals. Principal components analysis revealed a clear genetic division between animals for each population, and model-based clustering successfully detected evidence of admixture that matched aspects of their recorded history. For example, shared co-ancestry was detected, suggesting Boer goats have been introgressed into the Rangeland population. Further, allele frequency data successfully tracked the altered genetic profile that has taken place after 40 years of breeding Australian Cashmere goats using the Rangeland animals as the founding population. Genome-wide association mapping of the POLL locus revealed a strong signal on goat chromosome 1. The 769-kb critical interval contained the polled intersex syndrome locus, confirming the genetic basis in non-European animals is the same as identified previously in Saanen goats. Interestingly, analysis of the haplotypes carried by a small set of sex-reversed animals, known to be associated with polledness, revealed some animals carried the wild-type chromosome associated with the presence of horns. This suggests a more complex basis for the relationship between polledness and the intersex condition than initially thought while validating the application of the goat SNP50 BeadChip for fine-mapping traits in goat.

Uncontrolled admixture and loss of genetic diversity in a local Vietnamese pig breed

The expansion of intensive livestock production systems in developing countries has increased the introduction of highly productive exotic breeds facilitating indiscriminate crossbreeding with local breeds. In this study, we set out to investigate the genetic status of the Vietnamese Black H'mong pig breed by evaluating (1) genetic diversity and (2) introgression from exotic breeds. Two exotic breeds, namely Landrace and Yorkshire used for crossbreeding, and the H'mong pig population from Ha Giang (HG) province were investigated using microsatellite markers. Within the province, three phenotypes were observed: a White, a Spotted and a Black phenotype. Genetic differentiation between phenotypes was low (0.5-6.1%). The White phenotypes showed intermediate admixture values between exotic breeds and the Black HG population (0.53), indicating a crossbreed status. Management practices were used to predict the rate of private diversity loss due to exotic gene introgressions. After 60 generations, 100% of Black private alleles will be lost. This loss is accelerated if the admixture rate is increased but can be slowed down if the mortality rate (e.g., recruitment rate) is decreased. Our study showed that a large number of markers are needed for accurately identifying hybrid classes for closely related populations. While our estimate of admixture still seems underestimated, genetic erosion can occur very fast even through indiscriminate crossbreeding.

Genetic variation and population structure in Jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes

Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed.

Microsatellite DNA markers indicate three genetic lineages in East Asian indigenous goat populations

The genetic differentiation and phylogenetic relationships of 18 indigenous goat populations from seven East Asian countries were analysed based on data obtained from 26 microsatellite DNA markers. The mean number of alleles (MNA) per population ranged from 2.5 to 7.6, with an average of 5.8. Genetic variability estimated from MNA and heterozygosity (H(E) and H(O) ) were relatively low in coastal and island populations. A heterozygous deficiency within populations (F(IS) = 0.054, P < 0.001) and total inbreeding (F(IT) = 0.181, P < 0.01) were observed, and genetic differentiation in the populations (F(ST) ) was 13.4%. The results of Bayesian model-based clustering and a neighbour-joining tree based on Nei's genetic distance showed that Asian goat populations could be subdivided into at least the following three genetic clusters: East Asian, Southeast Asian and Mongolian. These results are in close accordance with conventional morphological and geographical classifications and migration history.

Genetic variability of six indigenous goat breeds using major histocompatibility complex-associated microsatellite markers

The present study aimed at analyzing the genetic variability of indigenous goat breeds (Capra hircus) using the MHC-associated microsatellite markers BF1, BM1818, BM1258, DYMS1, and SMHCC1. The following breeds were included: Chinese Xuhuai, Indian Changthangi and Pashmina, Kenyan Small East African (SEA) and Galla, and Albanian Vendi. To examine genetic variability, the levels of heterozigosity, degrees of inbreeding, and genetic differences among the breeds were analyzed. The mean number of alleles ranged from nine in the Galla to 14.5 in the Vendi breed. The mean observed heterozygosity and mean expected heterozygosity varied from 0.483 in the Vendi to 0.577 in the Galla breed, and from 0.767 in the SEA to 0.879 in the Vendi breed, respectively. Significant loss of heterozygosity (p < 0.01) indicated that these loci were not in Hardy-Weinberg equilibrium. The mean F(IS) values ranged from 0.3299 in the SEA to 0.4605 in the Vendi breed with a mean value of 0.3623 in all breeds (p < 0.001). Analysis of molecular variance indicated that 7.14% and 4.74% genetic variation existed among the different breeds and geographic groups, whereas 92.86% and 95.26% existed in the breeds and the geographic groups, respectively (p < 0.001). The microsatellite marker analysis disclosed a high degree of genetic polymorphism. Loss of heterozygosity could be due to genetic drift and endogamy. The genetic variation among populations and geographic groups does not indicate a correlation of genetic differences with geographic distance.

Characterization of casein gene complex and genetic diversity analysis in Indian goats

Milk protein polymorphism plays an important role in genetic diversity analysis, phylogenetic studies, establishing geographical diversity, conservation decision, and improving breeding goals. Milk protein polymorphism in Indian goat breeds has not been well studied; therefore, an investigation was carried out to analyze the genetic structure of the casein gene and milk protein diversity at six milk protein loci in nine Indian goat breeds/genetic groups from varied agro-climatic zones. Milk protein genotyping was carried out in 1098 individual milk samples by SDS-PAGE at alphaS1-CN (CSN1S1), beta-CN (CSN2), alphaS2-CN (CSN1S2), kappa-CN (CSN3), beta-LG, and alpha-LA loci. Indian goats exhibited alphaS1-casein A allele in higher frequency in the majority of breeds except Ganjam and local goats. The alphaS1-casein A allele frequencies varied from 0.45 to 0.77. A total of 16 casein haplotypes were observed in seven breeds and breed specific haplotypes were observed with respect to geographic region. The average number of alleles was lowest in Ganjam (1.66 +/- 0.81) and highest in Sirohi goats (2.50 +/- 1.05). Expected heterozygosity at six different loci demonstrated genetic diversity and breed fragmentation. Neighbor-Joining tree was built basing on Nei's distance. There was about 16.95% variability due to differences between breeds, indicating a strong subdivision. Principal component analysis was carried out to highlight the relationship among breeds. The variability among goat breeds was contributed by alphaS2-CN, beta-LG and alphaS1-CN. The Indian goats exhibited alphaS1-CN (CSN1S1) A allele in higher frequency in all the breeds indicating the higher casein yield in their milk.

Genetic diversity in farm animals--a review

Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.

Evolution of microsatellite loci in the adaptive radiation of Hawaiian honeycreepers

Previous studies have examined germ-line mutations to infer the processes that generate and maintain variability in microsatellite loci. Few studies, however, have examined patterns to infer processes that act on microsatellite loci over evolutionary time. Here, we examine changes in 8 dinucleotide loci across the adaptive radiation of Hawaiian honeycreepers. The loci were found to be highly variable across the radiation, and we did not detect ascertainment bias with respect to allelic diversity or allele size ranges. In examining patterns at the sequence level, we found that changes in flanking regions, repeat motifs, or repeat interruptions were often shared between closely related species and may be phylogenetically informative. Genetic distance measures based on microsatellites were strongly correlated with those based on mitochondrial DNA (mtDNA) sequences as well as with divergence time up to 3 My. Phylogenetic inferences based on microsatellite genetic distances consistently recovered 2 of the 4 honeycreeper clades observed in a tree based on mtDNA sequences but differed from the mtDNA tree in the relationships among clades. Our results confirm that microsatellite loci may be conserved over evolutionary time, making them useful in population-level studies of species that diverged from the species in which they were characterized as long as 5 Ma. Despite this, we found that their use in phylogenetic inference was limited to closely related honeycreeper species.

Evolutionary and phylogenetic significance of platypus microsatellites conserved in mammalian and other vertebrate genomes

Building on the recent publication of the first monotreme genome, that of the platypus, and the discovery that many platypus microsatellites are found in the genomes of three mammals (opossum, human, mouse) and two non-mammalian vertebrates (chicken, lizard), we investigated further the evolutionary conservation of microsatellites identified in the monotreme lineage and tested whether the conservation of microsatellites we observe in vertebrates has phylogenetic signal. Most conserved platypus microsatellites (75%) were found in one species, with the platypus sharing many more microsatellites with mammals than with reptiles (83% versus 30%). Within mammals, unexpectedly, many more platypus microsatellites had orthologues in the opossum genome than in that of either human or mouse, which was at odds with the very well supported view that monotremes diverged from a lineage containing both eutherians and marsupials (Theria hypothesis). We investigated the phylogenetic significance of microsatellite conservation through Bayesian and maximum parsimony tree reconstruction using presence/absence data of microsatellite loci conserved in a total of 18 species, including the platypus. Although models of evolution implemented in current phylogenetic reconstruction algorithms are not tailor-made for microsatellite data, we were able to construct vertebrate phylogenies that correspond well to the accepted mammalian phylogeny, with two of our three reconstructions supporting the Theria hypothesis. Our analysis provides ground for new theoretical development in phylogeny-based analyses of conserved microsatellite data.