Genetic diversity and phylogenetic relationship of nine sheep populations based on microsatellite markers

Abstract. The objective of this study was to assess the genetic diversity and phylogenetic relationship of nine sheep populations, including two famous high prolific populations and seven popular mutton populations raised in China. Overall, these sheep populations in this study exhibited a rich genetic diversity. Both the expected heterozygosity and Nei's unbiased gene diversity ranged from 0.64 to 0.75, with the lowest value found in Dorset sheep (DST) and the highest in Hu sheep (HUS) and Ba Han sheep (BAS). The polymorphic information content (PIC) varied between 0.59 in DST and 0.71 in HUS and BAS. Specifically, for individual breeds, the small-tail Han sheep (STH) and the four introduced populations did not display the expected diversity; therefore more attention should be paid to the maintenance of diversity during management of these populations. The results of un-weighted pair-group method (UPGMA) phylogenetic tree and structure analysis indicated that the nine investigated populations can be divided into two groups. Suffolk (SUF) and DST were clustered in one group, and the other group can be further divided into three clusters: German Mutton Merino (GMM)–BAS–Bamei Mutton sheep (BAM), HUS–STH and Du Han (DOS)–Dorper (DOP). This clustering result is consistent with sheep breeding history. TreeMix analysis also hinted at the possible gene flow from GMM to SUF. Together, an in-depth view of genetic diversity and genetic relationship will have important implications for breed-specific management.

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Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran

Archives Animal Breeding ◽

10.5194/aab-60-183-2017 ◽

2017 ◽

Vol 60 (3) ◽

pp. 183-189 ◽

Cited By ~ 9

Author(s):

Mohammad Taghi Vajed Ebrahimi ◽

Mohammadreza Mohammadabadi ◽

Ali Esmailizadeh

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Information Content ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Extraction Procedure ◽

Shannon Index ◽

Group Method ◽

Salting Out ◽

Pair Group

Abstract. Investigation of genetic relationship among populations has been traditionally based on the analysis of allele frequencies at different loci. The prime objective of this research was to measure the genetic polymorphism of five microsatellite markers (McMA2, BM6444, McMA26, HSC, and OarHH35) and study genetic diversity of 14 sheep types in Iran. Genomic DNA was extracted from blood samples of 565 individuals using an optimized salting-out DNA extraction procedure. The polymerase chain reaction (PCR) was successfully performed with the specific primers. Some locus–population combinations were not at Hardy–Weinberg equilibrium (P < 0. 05). The microsatellite analysis revealed high allelic and gene diversity in all 14 breeds. Pakistani and Arabi breeds showed the highest mean number of alleles (11.8 and 11 respectively), while the highest value for polymorphic information content was observed for the Arabi breed (0.88). A UPGMA (unweighted pair group method with arithmetic mean) dendrogram based on the Nei's standard genetic distance among studied breeds showed a separate cluster for Arabi and Pakistani breeds and another cluster for other breeds. The Shannon index (H0) for McMA2, BM6444, McMA26, HSC, and OarHH35 was 2.31, 2.17, 2.27, 2.04 and 2.18, respectively, and polymorphic information content (PIC) values were 0.88, 0.92, 0.87, 0.84, and 0.86 for McMA2, BM6444, McMA26, HSC, and OarHH35, respectively. The high degree of variability demonstrated within the studied sheep types implies that these populations are rich reservoirs of genetic diversity that must be preserved.

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Evaluation of Genetic Diversity among Persian Fig Cultivars by Morphological Traits and RAPD Markers

HortScience ◽

10.21273/hortsci11306-16 ◽

2018 ◽

Vol 53 (5) ◽

pp. 613-619 ◽

Cited By ~ 1

Author(s):

Ghazal Baziar ◽

Moslem Jafari ◽

Mansoureh Sadat Sharifi Noori ◽

Samira Samarfard

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Polymorphic Information Content ◽

Random Amplified Polymorphic Dna ◽

Hierarchical Cluster ◽

Fruit Trees ◽

Group Method ◽

Fars Province ◽

Pair Group

Ficus carica L. is one of the most ancient fruit trees cultivated in Persia (Iran). The conservation and characterization of fig genetic resources is essential for sustainable fig production and food security. Given these considerations, this study characterizes the genetic variability of 21 edible F. carica cultivars in the Fars Province using random amplified polymorphic DNA (RAPD) markers. The collected cultivars were also characterized for their morphological features. A total of 16 RAPD primers produced 229 reproducible bands, of which, 170 loci (74.43%) were polymorphic with an average polymorphic information content (PIC) value of 0.899. Genetic analysis using an unweighted pair-group method with arithmetic averaging (UPGMA) revealed genetic structure and relationships among the local germplasms. The dendrogram resulting from UPGMA hierarchical cluster analysis separated the fig cultivars into five groups. These results demonstrate that analysis of molecular variance allows for the partitioning of genetic variation between fig groups and illustrates greater variation within fig groups and subgroups. RAPD-based classification often corresponded with the morphological similarities and differences of the collected fig cultivars. This study suggests that RAPD markers are suitable for analysis of diversity and cultivars’ fingerprinting. Accordingly, understanding of the genetic diversity and population structure of F. carica in Iran may provide insight into the conservation and management of this species.

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Genetic diversity analysis in Brassica varieties through RAPD markers

Bangladesh Journal of Agricultural Research ◽

10.3329/bjar.v34i3.3976 ◽

1970 ◽

Vol 34 (3) ◽

pp. 493-503 ◽

Cited By ~ 5

Author(s):

KK Ghosh ◽

ME Haque ◽

S Parvin ◽

F Akhter ◽

MM Rahim

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Rapd Markers ◽

Gene Diversity ◽

Random Amplified Polymorphic Dna ◽

Arithmetic Mean ◽

Polymorphic Band ◽

Group Method ◽

Polymorphic Loci ◽

Pair Group

This investigation was aimed at exploring the genetic diversity and relationship among nine Brassica varieties, namely BARI Sharisha-12, Agrani, Sampad, BINA Sharisha-4, BINA Sharisha-5, BARI Sharisha-13, Daulot, Rai-5, Alboglabra using Random Amplified Polymorphic DNA (RAPD) markers. In total, 59 reproducible DNA bands were generated by four arbitrary selected primers of which 58 (98.03%) bands were proved to be polymorphic. These bands ranged from 212 to 30686 bp in size. The highest proportion of polymorphic loci and gene diversity values were 37.29% and 0.1373, respectively, for BARI Sharisha-12 and the lowest proportion of polymorphic loci and gene diversity values were 8.47% and 0.0318, 8.47% and 0.0382 for BINA Sharisha-4 and Rai-5, respectively. A dendrogram was constructed using unweighted pair group method of arithmetic mean (UPGMA). The result of cluster analysis indicated that the 9 accessions were capable of being classified into 2 major groups. One group consists of BARI Sharisha-12, Agrani, Sampad, Daulot, Rai-5, Alboglabra. where Daulot and Rai-5 showed the lowest genetic distance of 0.049. And another group contains BINA Sharisha-4, BINA Sharisha-5, and BARI Sharisha-1 3, where BINA Sharisha-5 and BARI sharisha-13 showed genetic distance of 0.071. Key Words: RAPD, Brassica, genetic distance, polymorphic band. DOI: 10.3329/bjar.v34i3.3976 Bangladesh J. Agril. Res. 34(3) : 493-5032, September 2009

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GENETIC DIVERSITY INAUS RICE LANDRACES OF BANGLADESH USING SSR MARKERS

Bangladesh Journal of Plant Breeding and Genetics ◽

10.3329/bjpbg.v30i1.36529 ◽

2017 ◽

Vol 30 (1) ◽

pp. 11-20 ◽

Cited By ~ 1

Author(s):

M. Khalequzzaman ◽

M. Z. Islam ◽

M. A. Siddique ◽

M. F. R. K. Prince ◽

E. S. M. H. Rashid ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Three Dimensional ◽

Group Method ◽

Breeding Programs ◽

Arithmetic Average ◽

Pair Group ◽

Rice Landraces ◽

Conservation Genetic ◽

Maximum Selection

Assessment of genetic diversity is essential for germplasm characterization, utilization and conservation. Genetic diversity of 31 Aus rice landraces of Bangladesh was assessed using 36 SSR (simple sequence repeats) markers. A total of 141 alleles were detectedand the number of alleles per locus ranged from two (RM1216, RM145, RM282, RM293, RM567and RM496) to 10 alleles (RM304), with an average of 3.92. The gene diversity varied from 0.06 (RM145) to 0.80 (RM304) with an average of 0.54 and the PIC values ranged from 0.06 (RM145) to 0.78 (RM304), with an average of 0.48.PIC value revealed that RM304 was the best marker for characterizing the studied Aus rice genotypes. The dendrogram from unweighted pair-group method with arithmetic average clustering of markers classified the genotypes into five major groups with a coefficient of 0.49. Two and three-dimensional graphical views of Principal Coordinate Analysis (PCA) revealed that the genotypes Hashikalmi, Chaina, Puitraaijang, Saithsail, Kuchmuch, Kalodhan, Ausdhan and Itcriewere found far away from the centroid of the cluster and can be selected as parents for further breeding programs.The results provided some useful implications for establishment of sovereignty of Bangladeshi rice gene pool. This information will provide maximum selection of diverse parents, background selection during backcross breeding programs and assist in broadening germplasm-based rice breeding programs in future.

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Genetic DiversityAssessment in Ten Aromatic Rice Varieties of Bangladesh

Plant Tissue Culture and Biotechnology ◽

10.3329/ptcb.v27i2.35027 ◽

2017 ◽

Vol 27 (2) ◽

pp. 217-225 ◽

Cited By ~ 1

Author(s):

Tahmina Islam ◽

Shinthia Rahman ◽

M Imdadul Hoque ◽

RH Sarker

Keyword(s):

Genetic Diversity ◽

Oryza Sativa L ◽

Group Method ◽

Aromatic Rice ◽

Arithmetic Means ◽

Rice Varieties ◽

Center Of Origin ◽

Pair Group ◽

Relationship Of ◽

Selection Of

The availability of molecular marker systems allowed estimating the relationships among various taxa. This study was aimed at assessing the genetic diversity among ten aromatic rice (Oryza sativa L.) pools from Bangladesh by means of randomly amplified polymorphic DNA (RAPD) markers. These varieties were evaluated for polymorphisms after amplification with 10 decamer primers. A total of 60 RAPD fragments were generated among the assessed varieties with a polymorphism percentage of 80. Cluster analysis by the unweighted pair group method of arithmetic means (UPGMA) showed that these 10 varieties could be placed into two groups with a similarity ranging from 65 to 86% depicting adjacent association between Rajbhog and Kalijira‐12, whereas Maloti belongs to a separate group maintaining maximum distance from rest of the varieties. The analysis revealed that the intervarietal genetic relationship of several varieties is related to their center of origin. As expected, most of the varieties have a narrow genetic base. The present results could be used for the selection of possible parents to generate a mapping population and utilized by the breeders for assessing the genetic diversity of rice genotypes.Plant Tissue Cult. & Biotech. 27(2): 217-225, 2017 (December)

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Assessment of genetic diversity in 35 Pisum sativum accessions using microsatellite markers

Canadian Journal of Plant Science ◽

10.4141/cjps2011-261 ◽

2012 ◽

Vol 92 (6) ◽

pp. 1075-1081 ◽

Cited By ~ 11

Author(s):

Sajjad Ahmad ◽

Manjit Singh ◽

Neil Dylan Lamb-Palmer ◽

Mark Lefsrud ◽

Jaswinder Singh

Keyword(s):

Genetic Diversity ◽

Pisum Sativum ◽

Microsatellite Markers ◽

Polymorphic Information Content ◽

Group Method ◽

Gene Pools ◽

Breeding Lines ◽

High Performing ◽

Pair Group ◽

Upgma Cluster Analysis

Ahmad, S., Singh, M., Lamb-Palmer, N. D., Lefsrud, M. and Singh, J. 2012. Assessment of genetic diversity in 35 Pisum sativum accessions using microsatellite markers. Can. J. Plant Sci. 92: 1075–1081. Field pea is an important Canadian pulse crop and therefore developing high-performing cultivars is critical for Canadian pea growers. Information about genetic diversity is a key component for the creation of novel and desirable germplasm to develop elite pea breeding lines. The objective of the present study is to assess genetic diversity in 35 diverse Pisum accessions using 15 polymorphic microsatellites located on different pea chromosomes. Microsatellites were found to be polymorphic, amplifying a total of 41 alleles and were able to differentiate all 35 Pisum genotypes. These markers were scored by their polymorphic information content (PIC), ranging from 0.055 (AA206) to 0.660 (AB72) with an average of 0.460, and by their discriminating power (D), which varied from 0.057 (AA206) to 0.679 (AB 72) with an average of 0.475. Genetic similarity values ranged from 0.074 (between Maple pea NZ and Line 45760) to 0.875 (between Galena and Dakota) with an average of 0.336. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis grouped the 35 pea accessions into two major clusters and eight sub-clusters. The majority of Canadian and European genotypes were grouped separately, suggesting both these groups are from genetically distinct gene pools. The genetically diverse groups identified in this study can be used to derive parental lines for pea breeding.

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Analysis of genetic diversity of African yam bean using SSR markers derived from cowpea

Plant Genetic Resources ◽

10.1017/s1479262115000064 ◽

2015 ◽

Vol 14 (1) ◽

pp. 50-56 ◽

Cited By ~ 3

Author(s):

Ndenum S. Shitta ◽

Michael T. Abberton ◽

Adenubi I. Adesoye ◽

Daniel B. Adewale ◽

Olaniyi Oyatomi

Keyword(s):

Genetic Diversity ◽

Polymorphic Information Content ◽

Group Method ◽

Arithmetic Average ◽

African Yam Bean ◽

Pair Group ◽

Ssr Primers ◽

Nutritional Qualities ◽

High Level ◽

Average Cluster

African yam bean, AYB (Sphenostylis stenocarpa Hochst. ex. A. Rich Harms), is a tuberous legume of tropical Africa. AYB has the potential to significantly boost food security due to its considerable nutritional qualities. However, the crop is underutilized. To efficiently utilize AYB genetic resources for its improvement, it is necessary to understand the crop's diversity. This study investigated the amplification ability of 36 cowpea simple sequence repeat (SSR) primers across AYB genomic DNA, extracted from 67 accessions. Thirteen (36%) of the cowpea SSRs showed transferability in AYB. Eight of these SSRs amplified above 60% of AYB accessions and generated 55 polymorphic fragments with an average of 6.9 per primer. Polymorphic information content ranged from 0.6691 to 0.8857 with an average of 0.7791. This study also assessed the genetic diversity within 67 AYB accessions using eight cowpea (Vigna unguiculata L. Walp)-derived SSR primers. The result revealed a high level of genetic diversity with simple matching coefficient ranging from 0.458 to 1.000. A dendrogram depicting three main clusters was generated based on unweighted pair group method with arithmetic average. Cluster 1 was the most diverse with a dissimilarity range of 0.517–1.000. The level of genetic diversity revealed in this study indicates that the studied AYB germplasm can be exploited for genetic improvement. Additionally, the transferable markers will aid AYB genome research and also make possible the comparative mapping between AYB and cowpea.

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Assessment of genetic diversity and differentiation among four indigenous Turkish sheep breeds using microsatellites

Archives Animal Breeding ◽

10.5194/aab-63-165-2020 ◽

2020 ◽

Vol 63 (1) ◽

pp. 165-172

Author(s):

Bahar Argun Karsli ◽

Eymen Demir ◽

Huseyin Goktug Fidan ◽

Taki Karsli

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Polymorphic Information Content ◽

Climatic Conditions ◽

Group Method ◽

Sheep Breeds ◽

Livestock Species ◽

Pair Group ◽

Breeding Programmes ◽

Study Population

Abstract. Conservation and breeding programmes of livestock species depend on determination of genetic diversity. Today in livestock species, microsatellite markers are commonly used to reveal population structure and genetic diversity in both breeds and varieties. In this study, population structure, genetic diversity, and differentiation among four native Turkish sheep breeds including Güney Karaman, Kangal, Norduz, and Karakas were assessed by using 21 microsatellite loci. By genotyping 120 individuals belonging to four sheep breeds, a total of 275 different alleles, 37 of which were private alleles, were observed across all loci. The mean number of alleles per breed ranged from 7.28 (Güney Karaman) to 8.09 (Karakas), while allelic richness ranged from 7.22 (Güney Karaman) to 7.87 (Karakas). Mean observed heterozygosity varied from 0.60 (Kangal) to 0.66 (Norduz and Karakas). The lowest pairwise FST value (0.084) was between Kangal and Karakas populations, while the highest pairwise FST value (0.142) was between Norduz and Karakas populations. Polymorphic information content (PIC) values, ranging from 0.71 (ETH10) to 0.91 (OarFCB304), were highly polymorphic (PIC > 0.5) and informative in studied populations. In the present study, the results of phylogenetic analysis were of importance, since all studied populations have been accepted as Akkaraman varieties till today. However, factorial correspondence and structure analysis, pairwise FST values, and an unweighted pair group method with arithmetic mean analysis (UPGMA) dendrogram revealed that Güney Karaman and Norduz populations have became genetically different from the Akkaraman breed due being raised in different parts of Turkey under different climatic conditions together with their breeding practices. Therefore, we recommend that more comprehensive molecular studies should be conducted to clarify genetic differentiation of Akkaraman sheep varieties.

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Morpho-agronomic Characters Under Drought Stress and Genetic Diversity on the Local Landraces of Cowpea [Vigna unguiculata (L.) Walp] From East Nusa Tenggara Province, Indonesia

Journal of Agricultural Science ◽

10.5539/jas.v13n3p17 ◽

2021 ◽

Vol 13 (3) ◽

pp. 17

Author(s):

Dwi Setyo Rini ◽

Anni Nuraisyah

Keyword(s):

Genetic Diversity ◽

Vigna Unguiculata ◽

Polymorphic Information Content ◽

Similarity Index ◽

Mantel Test ◽

Group Method ◽

Agronomic Characters ◽

Pair Group ◽

Drought Tolerant ◽

Matter Production

This study was performed to reveal the morpho-agronomic characters under drought and genetic diversity using SRAP (Sequence-related amplified polymorphism) marker on local landraces of cowpea (Vigna unguiculata (L). Walp) collected from East Nusa Tenggara Province, Indonesia. Data on drought response indexes according to the dry matter production of cowpea plants classified Carolina and Pinu Pahar as drought-sensitive and drought-tolerant cowpea genotypes, respectively. The assessment of the genetic diversity of cowpea genotypes was performed by using 25 SRAP combination primers. A total of 250 bands were produced by which 245 bands (98%) were polymorphic. The value of PIC (Polymorphic Information Content) of SRAP primers in this study varied from the highest value (0.97) to the lowest value (0.71) generated by primer pairs Me4-Em1 and Me3-Em4, respectively, with an average of PIC 0.87. An unweighted pair group method based on arithmetic averages (UPGMA) in this study was performed according to Nei and Li’s similarity index. The analysis of UPGMA and PCoA successfully separated Carolina and Pinu Pahar genotypes into different clusters. The result of the Mantel test showed that there was no significant correlation between the independent morpho-agronomic analysis and SRAP molecular matrix data.

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Genetic differentiation among sexually compatible relatives of Brassica napus L.

Genetika ◽

10.2298/gensr1302309p ◽

2013 ◽

Vol 45 (2) ◽

pp. 309-327 ◽

Cited By ~ 9

Author(s):

Barbara Pipan ◽

Jelka Sustar-Vozlic ◽

Vladimir Meglic

Keyword(s):

Gene Flow ◽

Brassica Napus ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Group Method ◽

Specific Gene ◽

Raphanus Raphanistrum ◽

Natural Habitats ◽

Brassica Napus L ◽

Pair Group

Analysis of gene flow between Brassica napus L. and its sexually compatible relatives that could be found in the wild in Slovenia was performed by microsatellite analysis using fifteen selected primer pairs. Genotypes included in the study were obtained from the field survey of sexually compatible relatives of B. napus in natural habitats around Slovenia and from reference collections. Two different wild species of all the presented sexually compatible relatives of B. napus were found in Slovenia, B. rapa and Sinapis arvensis. The reference genotypes included varieties and wild forms from internal collections as marketable seeds or from gene banks. Reference genotypes were represented by the following species and subspecies: B. napus ssp. napobrassica, B. napus ssp. napus, B. nigra, B. oleracea, B. rapa ssp. oleifera, Diplotaxis muralis; D. tenuifolia, Raphanus raphanistrum, R. sativus, R. sativus var. oleiformis, Rapistrum rugosum, S. alba and S. arvensis. Estimation of gene flow described by average number of migrants was 0.72 followed by 0.20 migrants. Due to the observed gene migrations, genetic drift and selection, Hardy-Weinberg equilibrium was not met. The mean number of alleles over all loci was 16.9, the average polymorphic information content was 0.43. We found four highly divergent and polymorphic loci (Na12-C08, Na10-A08, Ni3-G04b and BRMS-050) at statistically significant level (p<0.05) of gene flow detected. Over all gene diversity intra-individual among populations (0.55) was lower than inter-individual among population (0.77). The results of genetic linkages based standard genetic distance and unweighted pair group method with arithmetic mean clustering method, generally divided the genotypes in three divergent groups. Similar results were obtained by principal coordinate analysis where three main groups were constructed according to three factors. A real number of genetic clusters demonstrated a clear separation between populations, where only one was comprised from genotypes from other origins. The 30.7 % out-crossing rate of B. rapa and S. arvensis populations from filed survey represents the potential for spontaneous inter-and intra-specific gene flow under Slovenian production area.

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