Use of high‐density SNP data to identify patterns of diversity and signatures of selection in broiler chickens

Abstract

SummaryThe development of broiler chickens over the last 70 years has been accompanied by large phenotypic changes, so that the resulting genomic signatures of selection should be detectable by current statistical techniques with sufficiently dense genetic markers. Using two approaches, this study analysed high‐density SNP data from a broiler chicken line to detect low‐diversity genomic regions characteristic of past selection. Seven regions with zero diversity were identified across the genome. Most of these were very small and did not contain many genes. In addition, fifteen regions were identified with diversity increasing asymptotically from a low level. These regions were larger and thus generally included more genes. Several candidate genes for broiler traits were found within these ‘regression regions’, including IGF1,GPD2 and MTNR1AI. The results suggest that the identification of zero‐diversity regions is too restrictive for characterizing regions under selection, but that regions showing patterns of diversity along the chromosome that are consistent with selective sweeps contain a number of genes that are functional candidates for involvement in broiler development. Many regions identified in this study overlap or are close to regions identified in layer chicken populations, possibly due to their shared precommercialization history or to shared selection pressures between broilers and layers.

Accumulation of genetic variants associated with immunity in the selective breeding of broilers

“…By measuring dsRNA amounts and inflammatory response following digestion of dsRNA, it was established that dsRNA level in commensal Lactobacillales, which is higher than dsRNA amounts in pathogens such as Salmonella enterica serovar Typhimurium and Escherichia coli, is sufficient to induce anti-inflammatory signals via TLR3. Another study that used a high-density SNP array to investigate polymorphisms in a commercial broiler line also found that TLR3 falls within a region of positive selection [12]. This raises the interesting possibility that mutations that result in decreased TLR3 function may result in poor discrimination between commensal and pathogenic flora of the gut, that while resulting in dysbiosis, may nevertheless improve growth performance.…”

“…Note, we refer here to transcripts rather than genes since four of the five strategies rely on normalization of SNPs and SNP effects by transcript length. 12 The first strategy (Strategy 1) defines transcripts that have accumulated the greatest number of SNPs over the past 60 years. Here we compared increases in non-synonymous SNP density between the 1957 and the 1978 lines, and the 1978 and Ross308 lines.…”

“…In attempts to meet this 4 need, several groups have employed genomic approaches to characterize a diverse set of breeds, including native Taiwanese chickens [8], experimental lines that serve as animal models [9], as well as domestic layer and broiler lines [10,11]. Aside from identifying genes that dictate physical characteristics such as plumage or skin color, these studies have identified numerous selective sweeps [8,10,12], reflecting regions with reduced heterozygosity as a consequence of positive selection. Such sweeps have revealed the fixation of alleles predicted to be beneficial.…”

Evaluation of the genome in bird breeding

“…Проведен анализ данных высокой плотности SNP ли-нии бройлеров для обнаружения низкого разнообразия областей генома, сформированных примерно в течение 70летней селекции (Stainton et al, 2016). Идентифициро-вано семь регионов с нулевым разнообразием (гомозигот-ных районов).…”

Productive Performance in Local Chicken After Five Generations of Crossing and Selection for High Live Body Weight

“…Intensive genetic selection has been the method to improve economically traits in poultry production (Alnahhas et al, 2016). Stainton et al (2017) stated that the development of broiler chickens over the last 70 years has been accompanied by large phenotypic changes In addition, poultry breeding companies have used quantitative selection practices to improve productive performance the poultry industry today (Hunton, 2006). In broiler breeding program, mainline pedigree broiler populations, categorized into male and female lines, undergo continuous genetic selection to achieve higher improvements in the major economic traits.…”