PSIII-15 Genetic diversity and population structure in nine beef cattle sub-populations using whole genome SNP markers

Abstract Commercial beef cattle populations are rarely purebred. Understanding genetic diversity and population structure of crossbreds is important for future genetic improvement programs. Currently, an admixed beef cattle population comprised of British, Continental and Australian origin is being used for long-term research goals in understanding longevity, efficiency (reproductive and nutritional), and their interaction. This experiment aimed to assess the levels of genetic diversity and population structure among purebred (n = 6) and admixed (n = 3) sub-populations. A total of 727 animals were genotyped using the GeneSeek Genomic Profiler 150K. After quality checking, expected heterozygosity (HE) and polymorphism were calculated using 108,249 markers by sub-population. After LD-pruning, the remaining 19,316 SNP were used for pairwise fixation index (FST), analysis of molecular variance (AMOVA), and principle component analysis. The call rate for each sub-population ranged from 0.9866 ± 0.0351 to 0.9994 ± 0.0006. The lowest proportion (0.8527) of polymorphism was in the American Aberdeen (AA) and the highest proportion (1) was in the admixed populations. By sub-population, HE ranged from 0.3490 ± 0.1482 in AA to 0.3935 ± 0.1315 in Angus. The average nucleotide diversity over loci varied from 0.2976 ± 0.1444 in AA to 0.3872 ± 0.1879 in unknown parentage sub-population. The highest genetic differentiation was observed between AA and Continental breeds (Gelbvieh and Simmental) as FST estimates ranged from 0.1757 to 0.1789, respectively. Differences within individuals explained 98.15% of the total variance, whereas only -2.33% was due to differences among individuals within sub-populations. The first and second principal components (PC) explained 37.77% and 24.29% of the total variance, respectively. These PC show that admixed individuals clustered with animals of their primary breed. Therefore, this study suggests that clustering individuals according to their primary breed will assist in future genetic studies with this population and potentially future commercial genetic improvement programs.

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Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Scientific Reports ◽

10.1038/s41598-021-94802-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Grimar Abdiel Perez ◽

Pumipat Tongyoo ◽

Julapark Chunwongse ◽

Hans de Jong ◽

Anucha Wongpraneekul ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Germplasm Collection ◽

Snp Markers ◽

Fixation Index ◽

Breeding Programs ◽

Total Fixation ◽

Unrooted Phylogenetic Tree ◽

Luffa Acutangula ◽

Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

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Population Genetic Diversity and Structure of an Endangered Salicaceae Species in Northeast China: Chosenia arbutifolia (Pall.) A. Skv.

Forests ◽

10.3390/f12091282 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1282

Author(s):

Yu Wang ◽

Zhongyi Jiao ◽

Jiwei Zheng ◽

Jie Zhou ◽

Baosong Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Management Strategies ◽

Natural Populations ◽

Snp Markers ◽

Fixation Index ◽

Landscape Genomics ◽

Population Structure Analysis ◽

Genetic Diversity And Structure ◽

Chosenia Arbutifolia

Chosenia arbutifolia (Pall.) A. Skv. is a unique and endangered species belonging to the Salicaceae family. It has great potential for ornamental and industrial use. However, human interference has led to a decrease in and fragmentation of its natural populations in the past two decades. To effectively evaluate, utilize, and conserve available resources, the genetic diversity and population structure of C. arbutifolia were analyzed in this study. A total of 142 individuals from ten provenances were sampled and sequenced. Moderate diversity was detected among these, with a mean expected heterozygosity and Shannon’s Wiener index of 0.3505 and 0.5258, respectively. The inbreeding coefficient was negative, indicating a significant excess of heterozygotes. The fixation index varied from 0.0068 to 0.3063, showing a varied genetic differentiation between populations. Analysis of molecular variance demonstrated that differentiation accounted for 82.23% of the total variation among individuals, while the remaining 17.77% variation was between populations. Furthermore, the results of population structure analysis indicated that the 142 individuals originated from three primitive groups. To provide genetic information and help design conservation and management strategies, landscape genomics analysis was performed by investigating loci associated with environmental variables. Eighteen SNP markers were associated with altitude and annual average temperature, of which five were ascribed with specific functions. In conclusion, the current study furthers the understanding of C. arbutifolia genetic architecture and provides insights for germplasm protection.

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EVALUATION OF GENETIC DIVERSITY IN SELECTED BEEF BREEDS

AGROFOR ◽

10.7251/agreng2003039l ◽

2020 ◽

Vol 5 (3) ◽

Author(s):

Kristína LEHOCKÁ ◽

Radovan KASARDA ◽

Barbora OLŠANSKÁ ◽

Nina MORAVČÍKOVÁ

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Flow ◽

Beef Cattle ◽

Genetic Drift ◽

High Linkage Disequilibrium ◽

Snp Markers ◽

Data Set ◽

Population Structure Analysis ◽

Red Angus

The aim of the study was to estimate genetic drift and gene flow related to population structure and genetic diversity in selected beef cattle. For the evaluation of the genetic drift and gene flow among analysed populations, the Bayesian Population Structure Analysis and software Treemix were used. The genetic analysis included two cattle breeds bred in Slovakia (Charolais and Limousine). In addition to the Limousine and Charolais breeds, other beef cattle (Angus N = 90, Belgian Blue N = 4, Blonde d'Aquitaine N= 5, Hereford N = 98 and Red Angus N = 15) were analysed. The 50k Bead chip was used; the dataset consisted of 34,834 SNPs. To avoid detection bias, SNPs with high linkage disequilibrium (r2 = 0.05) were pruned from the database; the final data set consisted of 296 animals and 2,539 SNP markers. Our results reflected four modes of gene flow between Angus, Red Angus, Charolais, Limousine and Hereford. Analysed breeds were not confirmed to influence genetic make-up of Belgian Blue and Blonde d'Aquitaine populations. All migration edges reached weight values below 0.2. The only two migration edges higher in weight was observed, first between the ancestor of Limousine breed into Blond d'Aquitaine, and second among historical ancestor of Hereford breed into Red Angus. Our results reflect that the donor population has made a significant contribution to the recipient population.

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Analysis of Genetic Diversity and Population Structure of Pigeonpea [Cajanus cajan (L.) Millsp] Accessions Using SSR Markers

Plants ◽

10.3390/plants9121643 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1643

Author(s):

Didas Kimaro ◽

Rob Melis ◽

Julia Sibiya ◽

Hussein Shimelis ◽

Admire Shayanowako

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Genetic Improvement ◽

Polymorphic Information Content ◽

Geographic Origin ◽

Germplasm Collection ◽

Fixation Index ◽

Population Structure Analysis ◽

The Mean

Understanding the genetic diversity present amongst crop genotypes is an efficient utilization of germplasm for genetic improvement. The present study was aimed at evaluating genetic diversity and population structure of 48 pigeonpea genotypes from four populations collected from diverse sources. The 48 pigeonpea entries were genotyped using 33 simple sequence repeat (SSR) markers that are polymorphic to assess molecular genetic diversity and genetic relatedness. The informative marker combinations revealed a total of 155 alleles at 33 loci, with an average of 4.78 alleles detected per marker with the mean polymorphic information content (PIC) value of 0.46. Population structure analysis using model based revealed that the germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 53.3% of genetic variation existed within individuals. Relatively low population differentiation was recorded amongst the test populations indicated by the mean fixation index (Fst) value of 0.032. The Tanzanian pigeonpea germplasm collection was grouped into three major clusters. The clustering pattern revealed a lack of relationship between geographic origin and genetic diversity. This study provides a foundation for the selection of parental material for genetic improvement.

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Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

Plant Genetic Resources ◽

10.1017/s1479262121000034 ◽

2021 ◽

Vol 19 (1) ◽

pp. 20-28

Author(s):

Abush Tesfaye Abebe ◽

Adesike Oladoyin Kolawole ◽

Nnanna Unachukwu ◽

Godfree Chigeza ◽

Hailu Tefera ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Glycine Max ◽

Snp Markers ◽

Fixation Index ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Breeding Lines ◽

Soybean Germplasm ◽

Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

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Population structure and phylogenetic relationships in Brassica rapa L. subspecies by using isozyme markers

Brazilian Journal of Biology ◽

10.1590/1519-6984.226889 ◽

2020 ◽

Author(s):

R. H. Sammour ◽

M. A. Karam ◽

Y. S. Morsi ◽

R. M. Ali

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Brassica Rapa ◽

Phylogenetic Relationships ◽

Fixation Index ◽

Distribution Area ◽

Enzyme Analysis ◽

Breeding Programs ◽

Expected Heterozygosity ◽

Wide Range

Abstract The present study aimed to assess population structure and phylogenetic relationships of nine subspecies of Brassica rapa L. represented with thirty-five accessions cover a wide range of species distribution area using isozyme analysis in order to select more diverse accessions as supplementary resources that can be utilized for improvement of B. napus. Enzyme analysis resulted in detecting 14 putative polymorphic loci with 27 alleles. Mean allele frequency 0.04 (rare alleles) was observed in Cat4A and Cat4B in sub species Oleifera accession CR 2204/79 and in subspecies trilocularis accessions CR 2215/88 and CR 2244/88. The highest genetic diversity measures were observed in subspecies dichotoma, accession CR 1585/96 (the highest average of observed (H0) and expected heterozygosity (He), and number of alleles per locus (Ae)). These observations make this accession valuable genetic resource to be included in breeding programs for the improvement of oilseed B. napus. The average fixation index (F) is significantly higher than zero for the analysis accessions indicating a significant deficiency of heteozygosity. The divergence among subspecies indicated very great genetic differentiation (FST = 0.8972) which means that about 90% of genetic diversity is distributed among subspecies, while 10% of the diversity is distributed within subspecies. This coincides with low value of gene flow (Nm = 0.0287). B. rapa ssp. oleifera (turnip rape) and B. rapa ssp. trilocularis (sarson) were grouped under one cluster which coincides with the morphological classification.

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Population structure and genetic diversity analysis in Sali (Oryza sativa) rice germplasm of Assam using microsatellite markers

ORYZA- An International Journal on Rice ◽

10.35709/ory.2021.58.2.4 ◽

2021 ◽

Vol 58 (2) ◽

pp. 279-286

Author(s):

Sandhani Saikia ◽

Pratap Jyoti Handique ◽

Mahendra K Modi

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Genetic Improvement ◽

Crop Improvement ◽

Mean Value ◽

Diversity Analysis ◽

Rice Cultivars ◽

Improvement Program ◽

Information Index ◽

Improvement Programs

Genetic diversity is the source of novel allelic combinations that can be efficiently utilized in any crop improvement program. To facilitate future crop improvement programs in rice, a study was designed to identify the underlying genetic variations in the Sali rice germplasms of Assam using SSR markers. The 129 SSR markers that were used in the study amplified a total of 765 fragments with an average of 5.93 alleles per locus. The Shannon's Information Index was found to be in the range from 0.533 to 1.786. The Polymorphism Information Content (PIC) fell into the range from 0.304 to 0.691 with a mean value of 0.55. The overall FST value was found to be 0.519 that indicated the presence of genetic differentiation amongst the genotypes used in the study. The Sali population was divided into two clusters. The information obtained from the present study will facilitate the genetic improvement of Sali rice cultivars.

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Genetic diversity and population structure among goat genotypes in Kenya

10.1101/2020.07.06.189290 ◽

2020 ◽

Author(s):

Ruth W. Waineina ◽

Kiplangat Ngeno ◽

Tobias O. Otieno ◽

Evans D. Ilatsia

Keyword(s):

Population Structure ◽

Principal Component ◽

Genetic Distances ◽

Snp Markers ◽

Founder Population ◽

Good Opportunity ◽

Model Based Clustering ◽

Population Structuring ◽

Improvement Programs ◽

Genotype Clustering

AbstractPopulation structure and relationship information among goats is critical for genetic improvement, utilization and conservation. This study explored population structure and level of gene intermixing among four goat genotypes in Kenya: Alpine (n = 30), Toggenburg (n = 28), Saanen (n = 24) and Galla (n = 12). The population structuring and relatedness were estimated using principal component analysis utilizing allele frequencies of the SNP markers. Genotype relationships were evaluated based on the calculated Reynolds genetic distances. A phylogenetic tree was constructed to represent genotype clustering using iTOL software. Population structure was investigated using model-based clustering (ADMIXTURE) Genotypes relationships revealed four distinctive clusters: Alpine, Galla, Saanen and Toggenburg. The ADMIXTURE results revealed some level of gene intermixing among Alpine, Toggenburg and Saanen with Galla. Saanen goats were the most admixed genotype with 84%, 7% and 4% of its genome derived from Galla, Alpine and Toggenburg respectively. Alpine and Toggenburg goats shared some associations with the Galla goat; 10% and 1% respectively. The association of Galla with other genotypes was anticipated since Galla goat was used as the founder population for crossbreeding with Saanen, Alpine and Toggenburg breed. The genetic variations among the goat genotypes observed, will provide a good opportunity for sustainable utilization, conservation and future genetic resource improvement programs in goat genotypes in Kenya.

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Genetic Diversity Analysis of 53 Indonesian Rice Genotypes using 6K Single Nucleotide Polymorphism Markers

Jurnal AgroBiogen ◽

10.21082/jbio.v14n1.2018.p1-10 ◽

2018 ◽

Vol 14 (1) ◽

pp. 1

Author(s):

Joko Prasetiyono ◽

Nurul Hidayatun ◽

Tasliah Tasliah

Keyword(s):

Genetic Diversity ◽

Morphological Characters ◽

Snp Markers ◽

Japonica Rice ◽

Rice Varieties ◽

Tropical Japonica ◽

Rice Chromosomes ◽

Improvement Programs ◽

Rice Genotypes ◽

Genotypic Mixtures

<p>Indonesia is rich in rice genetic resources, however, only a small number has been used in variety improvement programs. This study aimed to determine the genetic diversity of Indonesian rice varieties using 6K SNP markers. The study was conducted at ICABIOGRAD for DNA isolation and IRRI for SNP marker analysis. Genetic materials were 53 rice genotypes consisting of 49 varieties and 4 check genotypes. SNP markers used were 6K loci. Results showed that among the markers analyzed, only 4,606 SNPs (76.77%) were successfully read. The SNP markers covered all twelve rice chromosomes of 945,178.27 bp. The most common allele observed was GG, whereas the least allele was TG. Dendrograms of the 53 rice varieties analyzed with 4,606 SNPs demonstrated several small groups containing genotypic mixtures between indica and japonica rice, and no groups were found to contain firmly indica or japonica type. Structure analysis (K = 2) with value of 0.8 showed that the 53 rice varieties were divided into several groups and each group consisted of 4 japonica, 2 tropical japonica, 46 indica, and 1 aus rice type, respectively. IR64 and Ciherang proved to have an indica genome, while Rojolele has japonica one. Dupa and Hawara Bunar, usually grouped into tropical japonica rice, were classified as indica type, and Hawara Bunar has perfectly 100% indica type. The results of this study indicated that rice classification (indica-japonica) which is usually classified based only on morphological characters, e.g. grain and leaf shapes, is not enough and classification based on SNP markers should be considered for that purpose.</p>

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Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

Plants ◽

10.3390/plants9091190 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1190 ◽

Cited By ~ 1

Author(s):

Eunju Seo ◽

Kipoong Kim ◽

Tae-Hwan Jun ◽

Jinsil Choi ◽

Seong-Hoon Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Principal Component ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Useful Knowledge ◽

Population Structure Analysis ◽

Group 3 ◽

Genetic Diversity Study

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.

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