Genetic diversity and population structure of sweet orange [Citrus sinensis (L.) Osbeck] germplasm of India revealed by SSR and InDel markers

Sweet orange (Citrus sinensis (L.) Osbeck) is an important commercial citrus fruit crop, cultivated in India and across the world. In India most of the cultivated sweet orange species were introduced varieties. In this study, we used two molecular markers, SSR and InDels, to understand the genetic diversity and population structure of seventy-two sweet orange genotypes. Genetic parameters consisted of a total number of alleles, a number of polymorphic alleles (effective alleles); genetic diversity (G.D.), expected heterozygosity (He), and the polymorphic information content (PIC) were calculated based on molecular data. Two dendrograms were constructed based on the InDels and SSR. In both the cases, they formed three major clusters showing various degrees of variations with respect to members of the clusters. Population structure analysis revealed the presence of two distinct subpopulations. Therefore, in order to address various challenges and develop sweet orange varieties with desirable traits, there is a need to broaden the genetic base of sweet orange through the intensive collection in the northeastern region. These results of intraspecific genetic variability of the collections will dictate the path for the sweet orange breeding and conservation programs in India.

Development of SSR Markers and Genetic Diversity Evaluation of Mycocentrospora Acerina Causing Round Spot of Panax Notoginseng in Yunan Province, China

Sanqi round spot, which is caused by Mycocentrospora acerina, is a destructive disease limits the production of Panax notoginseng in Yunnan province of China. However, the disease has not been studied comprehensively. In the current study, we identify M. acerina polymorphic microsatellite markers using CERVUS 3.0 and compare the genetic diversity of its isolates from P. notoginseng round spot using Simple Sequence Repeat (SSR) markers and polyacrylamide gel electrophoresis. Thirty-two SSR markers with good polymorphism were developed using MISA and CERVUS 3.0. The genetic diversity of 187 M. acerina isolates were evaluated using 14 representative SSR primers, and the polymorphic information content values of 14 sites ranged from 0.813 to 0.946, with a total of 264 alleles detected at 14 microsatellite loci. The average expected heterozygosity was 0.8967. The genetic diversity of M. acerina in Yunnan province does not reflect geographic specificity.

Using of Microsatellites to Study the Genetic Polymorphisms of SRYm18 Region in Iraqi Sheep

The origin of animals is usually determined by their paternal genotypes of the genes on the Y chromosome. In addition to the genes and their polymorphisms in the genome of mitochondria that are inherited through dams. In view of the lack of studies focusing on the genes of the Y chromosome in the world and their absence in Iraq. The aim of the present study was to identify the multiple genetic polymorphisms of the SRYM18 gene in the Arabi and Awassi sheep raised in Iraq. The study was conducted in the Genetic Engineering Laboratories - College of Agriculture, University of Basra, as well as in the Basra Genome Laboratory. The amplification of the SRYM18 gene showed genetic polymorphisms and gave a gene segment of (103-880) bp. The number of alleles of the SRYm18 gene was 13 alleles in the Arabi and 16 alleles in the Awassi breeds. The equilibrium test showed that the two breeds were under equilibrium. The two breeds were identical with nine alleles, while the number of special alleles for the Arabi breed was two, while the Awassi breed was distinguished by five. The number of rare alleles reached 20, of which seven were of the Arabi breed, and 13 of them were of the Awassi breed. Mean expected heterozygosity was 0.6386 with nonsignificant Fis for Arabi breed (0.1541) but significant for Awassi breed (0.2213). Mean neutrality was close to lower bound (0.1721) and (0.1270) for Arabi and Awassi breeds respectively

Development And Identification of 131 SNP Markers In Sthenoteuthis Pteropus (Steenstrup)

The orangeback flying squid, Sthenoteuthis pteropus, is a species of significant potential value that is widely distributed in the tropical and temperate waters of the Atlantic Ocean. There have been no reports of the population genetics and effective molecular markers for this species due to a lack of reliable information regarding its genetic structure and its many individual differences, as well as its complex and changeable life history. Therefore, the development of auxiliary molecular markers would contribute to the development, sustainable utilization, and protection of the species. In this study, 131 novel single nucleotide polymorphism (SNP) markers were developed by double digest restriction-site associated DNA sequencing (dd-RAD). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.00 to 0.80 and 0.18 to 0.50, respectively. The polymorphism information content (PIC) value ranged from 0.18 to 0.50. None of the marker locations significantly deviated from the Hardy-Weinberg equilibrium (p >0.05) after a Bonferroni correction. These polymorphic SNPs will be important in the further analysis of the population heredity of S. pteropus and its scientific management.

Characterization and Genetic Diversity of Taif Chicken Ecotype Using Dense Microsatellites Panel

The current study is the first comprehensive investigation to address the native chicken ecotypes of the Taif region to unravel the genetic diversity using a dense panel of 40 microsatellites (SSR). Blood samples were collected from 25 hens randomly sampled from a village farm at Taif governorate. A total of 147 alleles were detected, with an average of 3.7 alleles per locus. The overall mean of polymorphic information content (PIC) was 0.43. The average observed heterozygosity (Hobs) of 0.28 was lower than the expected heterozygosity (Hexp) of 0.48. Out of 40l ocionly11 loci showed insignificant deviation from Hardy Weinberg expectation. The ecotypes showed low genetic diversity (HS = 0.65) and a high level of inbreeding (FIS= 0.75). The high FIS is indicative of the endangerment potentiality of this ecotype. Nine SSR showed an inbreeding coefficient of one. The significant estimate of the inbreeding coefficient of the present study calls for an immediate breeding plan to preserve such endangered ecotypes. Results of the present study will provide an initial guide to design further investigations for the development of sustainable genetic improvement and conservation programs for the Taif ecotype genetic resources.

Elucidating Genetic Diversity in Apricot (Prunus armeniaca L.) Cultivated in the North-Western Himalayan Provinces of India Using SSR Markers

Apricot (Prunus armeniaca L.) is an important temperate fruit crop worldwide. The availability of wild apricot germplasm and its characterization through genomic studies can guide us towards its conservation, increasing productivity and nutritional composition. Therefore, in this study, we carried out the genomic characterization of 50 phenotypically variable accessions by using SSR markers in the erstwhile States of Jammu and Kashmir to reveal genetic variability among accessions and their genetic associations. The genetic parameter results revealed that the number of alleles per locus (Na) ranged from 1 to 6 with a mean Na value of 3.89 and the mean effective number of alleles (Ne) per locus 1.882 with a range of 1.22 to 2. Similarly, the polymorphic information content (PIC) values ranged from 0.464 to 0.104. The observed heterozygosity (Ho) (0.547) was found to have higher than expected heterozygosity (He) (0.453) with average heterozygosity of 0.4483. The dendrogram clustered genotypes into three main clades based on their pedigree. The population structure revealed IV sub-populations with all admixtures except the III sub-population, which was mainly formed of exotic cultivars. The average expected heterozygosity (He) and population differentiation within four sub-populations was 1.78 and 0.04, respectively, and explained 95.0% of the total genetic variance in the population. The results revealed that the SSR marker studies could easily decrypt the genetic variability present within the germplasm, which may form the base for the establishment of good gene banks by reducing redundancy of germplasm, selection of parents for any breeding program.

Potential effects of life history on demographic genetic structure in stage-structured plant populations

Standing genetic variation, or genetic diversity, is a source of adaptive evolution, and is crucial for long-term population persistence under environmental changes. One empirical method to predict the temporal dynamics of standing genetic variation in age- or stage-structured populations is to compare genetic diversity and composition among age/stage classes. The resultant within-population genetic structure, sometimes referred to as demographic genetic structure, has been regarded as a proxy of potential genetic changes that accompany sequential generation turnover. However, especially in stage-structured plant populations, individuals in more juvenile stages do not necessarily represent future populations, as they might die, stop growing, or retrogress over the course of life history. How demographic genetic structure is subjected to life history and whether it is a good proxy of temporal genetic dynamics had remained unclear. Here, we developed a matrix model which well describes temporal dynamics of expected heterozygosity, a common proxy of genetic diversity, for a neutral locus in stage-structured populations under equilibrium assumption. Based on the model, two indices of demographic genetic structure were formulated: relative ratio of expected heterozygosity and genetic differentiation among stage classes. We found that the two indices were largely determined by stable stage distribution and population size, and that they did not show clear correlations with the change rate of genetic diversity, indicating that inferring future genetic diversity from demographic genetic structure conventionally is misleading. Our study facilitates reliable interpretation on empirical demographic genetic data.

Assessment of Genetic Diversity and Relationship of the Two Sanga Type Cattle of Botswana Based on Microsatellite Markers

The study was performed to evaluate genetic variation on two Sanga type cattle found in Botswana; Tswana and Tuli using twelve microsatellite markers. All amplified loci were polymorphic with 75 and 77 alleles genotyped in the Tswana and Tuli populations, respectively. The total number of alleles per locus ranged from 2 (BM1818) to 10 (TGLA227) with total mean of 6.25 for Tswana and 6.43 for Tuli population. Almost all the markers showed high polymorphic information content (PIC) apart from BM1818 (0.375) and INTRA23 (0.393) which were moderately informative in Tswana population. Most of the markers were in Hardy-Weinberg equilibrium except for CSSRM60 and CSSM66 loci in Tswana population and ETH10, ETH225 and CSSM66 loci in Tuli population. A total of 103 unique alleles were genotyped across the two breeds with 49-shared, and 26 and 28 were unique to Tswana and Tuli populations, respectively. The expected heterozygosity (He) values were higher than the observed heterozygosity (Ho) in both populations; Tswana (He=0.7895±0.033 vs Ho=0.631±0.091) and Tuli (He=0.8123±0.033 vs Ho=0.556±0.021). The inbreeding coefficient was 0.200±0.002 and 0.332±0.001 in Tswana and Tuli populations, respectively. Analysis of molecular variance revealed 6.8% of the total genetic variation corresponding to differences between the two breeds and 93.2% within populations. The genetic identity between the two breeds was 56% and there were similar levels of multilocus heterozygosity and allelic diversity in the two breeds. The use of Tswana and Tuli breeds in a crossbreeding program is likely to result in minimal heterosis and therefore not recommended.

Assessment of Genetic Diversity and Identification of Core Germplasm of Pueraria in Guangxi Using SSR Markers

Pueraria is not only one of the most important commercial crops, but a health supplement for human being. There are abundant Pueraria germplasm resources and a large planting scale in Guangxi. However, the genetic diversity and core germplasm of the Pueraria species in Guangxi are rarely understood. In this study, 272 individuals of Pueraria species in Guangxi combined with 23 pairs of simple sequence repeat primers were used to evaluate the genetic diversity and construct core germplasm. Ultimately, 118 alleles were identified and 112 alleles were polymorphic; the mean expected heterozygosity per locus is 0.1841, and the mean gene flow Nm is 1.7690. 272 individuals were divided into two main clusters, which is consistent with the results based on principal coordinate analysis and STRUCTURE cluster analysis. We proposed a core collection of 20 Pueraria accessions capturing 105 alleles. There was a non-significant relationship between genetic distance and geographical distance. The results could provide theoretical support for the scientific conversation of Pueraria genetic resources, which can serve as the basis for the breeding program of Pueraria.

Genetic diversity of Aquilaria microcarpa Baill. in Kalimantan using RAPD Markers

Aquilaria microcarpa is one of the agarwood producers species included in the endangered category based on the IUCN red list. Kalimantan is one of the natural distributions of this species. The high demand for agarwood causes this species to be commonly cultivated in community plantations. This study aimed to assess the genetic diversity of A. microcarpa using the RAPD markers. Forty-four leaf samples of A.microcarpa were collected from the local community in Gumbil (South Kalimantan) and Sanggau (West Kalimantan). The results showed that 9 out of 24 RAPD primers were stable in amplification, and polymorphic totally consisted of 49 polymorphic loci. The values of unbiased expected heterozygosity (uHE) were at a low level; they ranged between 0.152 (Gumbil II) to 0.249 (Gumbil I). The average genetic distance between Gumbil and Sanggau is 0.1733, related to their geographic distance. A private allele was only found at Gumbil at locus G18/540 and Sanggau at locus G18/550, respectively. A great DA value between Gumbil I and II showed that the plantations originated from different seed sources. AMOVA also verified the differences between the two populations. This finding has important implications in managing plantations and seeds transfer.