Dataset Information

Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits.

ABSTRACT: Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.

SUBMITTER: Li X

PROVIDER: S-EPMC7272655 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits.

Li Xin X Yang Ji J Shen Min M Xie Xing-Long XL Liu Guang-Jian GJ Xu Ya-Xi YX Lv Feng-Hua FH Yang Hua H Yang Yong-Lin YL Liu Chang-Bin CB Zhou Ping P Wan Peng-Cheng PC Zhang Yun-Sheng YS Gao Lei L Yang Jing-Quan JQ Pi Wen-Hui WH Ren Yan-Ling YL Shen Zhi-Qiang ZQ Wang Feng F Deng Juan J Xu Song-Song SS Salehian-Dehkordi Hosein H Hehua Eer E Esmailizadeh Ali A Dehghani-Qanatqestani Mostafa M Štěpánek Ondřej O Weimann Christina C Erhardt Georg G Amane Agraw A Mwacharo Joram M JM Han Jian-Lin JL Hanotte Olivier O Lenstra Johannes A JA Kantanen Juha J Coltman David W DW Kijas James W JW Bruford Michael W MW Periasamy Kathiravan K Wang Xin-Hua XH Li Meng-Hua MH

Nature communications 20200604 1

Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, br ...[more]

PMID: 32499537

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Project description:BackgroundPepper is a major crop species of the Solanaceae family, largely appreciated for its high nutritional and healthy contribution to human diets. In the Mediterranean basin, the favorable pedoclimatic conditions enhanced the selection of several diversified landraces cultivated pepper (Capsicum annuum), for whom Italy can be considered a main pole of diversification. Hence, a survey of traditional C. annuum genetic resources is essential for deep understanding of such diversity and for applications in genomics assisted breeding. Here, we report whole-genome resequencing analyses of two sweet and two pungent genotypes highly diffused in South Italy and representative of the variability for shape, colour and nutritional properties.ResultsThe four genomes were reconstructed at a chromosomal scale using a reference-guided approach, based on a dataset of 2.6 billion paired-end reads, corresponding to 20× genome coverage and a mapping rate above 99% for a final genomes size of approximately 3 Gb. After five iterations of variant calling, a total of 29,258,818 single nucleotide polymorphisms (SNPs) and 1,879,112 InDels, were identified. Substantial differences were observed among the four genomes based on geographical origin, with chromosomes 9 and 11 showing more polymorphisms in the accessions with higher fruit weight and absence of pungency. Among the identified variants, a small private indel (T - > TA) shared between sweet and big fruits accessions induces a frameshift with the generation of a new stop codon in a gene annotated as extensin, whereas two private SNPs within hot types were identified in 1-aminocyclopropane-1-carboxylate oxidase (ACO), a key gene involved in fruit ripening. The estimation of repetitive elements highlights a preponderant presence of Long Terminal Repeats (LTRs), the majority of which belonged to Gypsy superfamily. By comparing the four genomes with publicly available references including 'CM334' and Zunla-1 highlight the presence of 49,475 shared gene families.ConclusionsThe new genomic sequences aim to enrich the whole genome information of pepper local varieties, providing a valuable tool for precision gene mapping, marker discovery, comparative studies. Such knowledge widens the frontiers to understand the selection history of Italian pepper landraces toward the recognition of specificity local agri-food products marks.

Dataset Information

Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits.

Publications

Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits.

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