Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds

Indigenous cattle play a vital role in subsistence and livelihood of pastoral producers in Eritrea. In order to optimally utilize and conserve these valuable indigenous cattle genetic resources, the need to carry out an inventory of their genetic diversity was recognized. This study assessed the genetic variability, population structure and admixture of the indigenous cattle populations (ICPs) of Eritrea using a genotype by sequencing (GBS) approach. The authors genotyped 188 animals, which were sampled from 27 cattle populations in three diverse agro-ecological zones (western lowlands, highlands and eastern lowlands). The genome-wide analysis results from this study revealed genetic diversity, population structure and admixture among the ICPs. Averages of the minor allele frequency (AF), observed heterozygosity (HO), expected heterozygosity (HE), and inbreeding coefficient (FIS) were 0.157, 0.255, 0.218, and -0.089, respectively. Nei’s genetic distance (Ds) between populations ranged from 0.24 to 0.27. Mean population differentiation (FST) ranged from 0.01 to 0.30. Analysis of molecular variance revealed high genetic variation between the populations. Principal component analysis and the distance-based unweighted pair group method and arithmetic mean analyses revealed weak substructure among the populations, separating them into three genetic clusters. However, multi-locus clustering had the lowest cross-validation error when two genetically distinct groups were modelled. This information about genetic diversity and population structure of Eritrean ICPs provided a basis for establishing their conservation and genetic improvement programmes. Keywords: genetic variability, molecular characterization, population differentiation

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Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03965-1 ◽

2021 ◽

Author(s):

Xiao Zhang ◽

Yonghui Zhu ◽

Karl A. G. Kremling ◽

M. Cinta Romay ◽

Robert Bukowski ◽

...

Keyword(s):

Genetic Diversity ◽

Functional Impact ◽

Genome Wide Analysis ◽

Maize Population ◽

Genome Wide

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Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds

Animals ◽

10.3390/ani10081441 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1441

Author(s):

Filippo Cendron ◽

Francesco Perini ◽

Salvatore Mastrangelo ◽

Marco Tolone ◽

Andrea Criscione ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Conservation Status ◽

Geographical Area ◽

Snp Array ◽

Local Economy ◽

Conservation Strategies ◽

Snp Analysis ◽

Runs Of Homozygosity ◽

Chicken Breeds

The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.

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Genetic Variability in Local and Imported Germplasm Chicken Populations as Revealed by Analyzing Runs of Homozygosity

Animals ◽

10.3390/ani10101887 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1887

Author(s):

Natalia V. Dementieva ◽

Andrei A. Kudinov ◽

Tatiana A. Larkina ◽

Olga V. Mitrofanova ◽

Artyom P. Dysin ◽

...

Keyword(s):

Genetic Variability ◽

Germplasm Collection ◽

Whole Genome ◽

Runs Of Homozygosity ◽

Breeding Programs ◽

Genome Wide Analysis ◽

Genome Wide ◽

Rare And Endangered ◽

Chicken Breeds ◽

Conservation Breeding

Preserving breed uniqueness and purity is vitally important in developing conservation/breeding programs for a germplasm collection of rare and endangered chicken breeds. The present study was aimed at analyzing SNP genetic variability of 21 small local and imported purebred and F1 crossbred populations and identifying crossbreeding events via whole-genome evaluation of runs of homozygosity (ROH). The admixture models more efficiently reflected population structure, pinpointing crossbreeding events in the presence of ancestral populations but not in their absence. Multidimensional scaling and FST-based analyses did not discriminate properly between purebred populations and F1 crossbreds, especially when comparing related breeds. When applying the ROH-based approach, more and longer ROHs were revealed in purebred individuals/populations, suggesting this as an effective implement in genome-wide analysis of germplasm breed purity.

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