Natural adaptation and human selection of northeast African sheep genomes

African sheep manifest diverse but distinct physio-anatomical traits, which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous northeast African sheep genomes sequenced at an average depth of ∼54× for 130 samples (Ethiopia, Libya) and ∼20× for 20 samples (Sudan). These represented sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups corresponding to altitudinal geographic origins, tail morphotypes and possible historical introduction and dispersal of the species into and across the continent. Running admixture at higher levels of K (6 ≤ K ≤ 25), revealed cryptic levels of genome intermixing as well as distinct genetic backgrounds in some populations. Comparative genomic analysis identified targets of selection that spanned conserved haplotype structures overlapping clusters of genes and gene families. These were related to hypoxia responses, ear morphology, caudal vertebrae and tail skeleton length, and tail fat-depot structures. Our findings provide novel insights underpinning morphological variation and response to human-driven selection and environmental adaptation in African indigenous sheep

Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep

Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, which have impacted on the variation of its indigenous livestock. Here, we investigate autosomal genome-wide profiles of 11 Ethiopian indigenous sheep populations using the Illumina Ovine 50 K SNP BeadChip assay. Sheep from the Caribbean, Europe, Middle East, China, and western, northern and southern Africa were included to address globally, the genetic variation and history of Ethiopian populations. Population relationship and structure analysis separated Ethiopian indigenous fat-tail sheep from their North African and Middle Eastern counterparts. It indicates two main genetic backgrounds and supports two distinct genetic histories for African fat-tail sheep. Within Ethiopian sheep, our results show that the short fat-tail sheep do not represent a monophyletic group. Four genetic backgrounds are present in Ethiopian indigenous sheep but at different proportions among the fat-rump and the long fat-tail sheep from western and southern Ethiopia. The Ethiopian fat-rump sheep share a genetic background with Sudanese thin-tail sheep. Genome-wide selection signature analysis identified eight putative candidate regions spanning genes influencing growth traits and fat deposition (NPR2, HINT2, SPAG8, INSR), development of limbs and skeleton, and tail formation (ALX4, HOXB13, BMP4), embryonic development of tendons, bones and cartilages (EYA2, SULF2), regulation of body temperature (TRPM8), body weight and height variation (DIS3L2), control of lipogenesis and intracellular transport of long-chain fatty acids (FABP3), the occurrence and morphology of horns (RXFP2), and response to heat stress (DNAJC18). Our findings suggest that Ethiopian fat-tail sheep represent a uniquely admixed but distinct genepool that presents an important resource for understanding the genetic control of skeletal growth, fat metabolism and associated physiological processes

Inheritance and Molecular Mapping of Soybean Aphid Resistance in Soybean Germplasm Accession PI 603432B

Soybean aphid (Aphis glycines Matsumura) has been found colonizing soybean (Glycine max (L.) Merr.) plants in the upper Midwestern United States since 2000. Genetic characterization of resistance to soybean aphids helps to develop new resistant cultivars to protect soybean production from pest damage. The objective of this study is to analyze the inheritance of soybean aphid resistance in the soybean germplasm accession PI 603432B, and to map the location of the resistance gene(s). Two populations were formed by crossing the resistant PI 603423B with two susceptible varieties (MN0602CN and MN0081). The F2 plants and F2:4 lines from each cross were screened for aphid resistance in the field and greenhouse. The segregation for aphid resistance in the F2 and F2:4 populations derived from both crosses appeared to fit a single dominant gene model in inheritance. To determine whether the PI 603432B has the same gene(s) as those previously identified in other germplasm lines (plant introductions, PIs), 12 simple sequence repeat (SSR) markers which were previously reported to be associated with soybean aphid resistance were screened using bulk segregate analysis (BSA). The data from the SSR marker screening indicated that PI 603432B carried the same or similar gene as resistance gene Rag2 identified in PI 243540. The gene/QTL was mapped to a region on the linkage group F between SSR markers Sct_033 and Satt510. This information will be useful to facilitate breeding for aphid resistance in soybean