【摘要】：本研究旨在評價(jià)基因庫與保種場兩個(gè)鹿苑雞保種群的保種現(xiàn)狀。利用RAD-seq簡化基因組測序鑒定基因庫與保種場兩個(gè)鹿苑雞群體的SNP標(biāo)記,通過計(jì)算遺傳統(tǒng)計(jì)量,比較分析兩個(gè)群體的遺傳差異。結(jié)果,經(jīng)過兩步數(shù)據(jù)質(zhì)控,在基因庫與保種場兩個(gè)鹿苑雞群體中分別鑒定出SNPs標(biāo)記395 021個(gè)和428 314個(gè),兩個(gè)群體的平均雜合度Ho分別為0.211 1和0.206 8,群體間的遺傳分化系數(shù)Fst為0.005 6;在Structure模型聚類分析中兩個(gè)群體始終聚為一類,沒有個(gè)體分離出來,表明兩個(gè)鹿苑雞群體未發(fā)生顯著遺傳分化(P0.05)。兩個(gè)群體的近交系數(shù)Fis分別為0.178 8和0.193 5,相對較高的近交水平可能是由于起始基礎(chǔ)群規(guī)模較小(搶救性保護(hù))所導(dǎo)致的。進(jìn)一步的選擇信號分析發(fā)現(xiàn),兩個(gè)鹿苑雞群體在1、2、5、Z等染色體區(qū)域(位點(diǎn))上存在一定分化,通過F_(st)和θ_π檢驗(yàn)鑒定出58個(gè)受選擇區(qū)域,篩選到96個(gè)受選擇候選基因。GO和KEGG分析表明,這些差異基因主要富集在能量代謝、信號傳遞、應(yīng)激免疫反應(yīng)等調(diào)控通路。利用全基因組SNP標(biāo)記信息可以更全面地評價(jià)保種現(xiàn)狀,研究結(jié)果為進(jìn)一步優(yōu)化鹿苑雞保種技術(shù)方案提供了依據(jù)。
[Abstract]:The purpose of this study was to evaluate the current status of conservation of chicken populations in gene pool and seed conservation farm. The SNP markers of two populations of Luyuan chicken were identified by RAD-seq simplified genome sequencing. The genetic differences between the two populations were compared and analyzed by calculating the genetic statistics. The results showed that after two step data quality control, 395,021 SNPs markers and 428,314 SNPs markers were identified in two populations of Luyuan chicken in gene pool and seed preservation farm, respectively. The average heterozygosity Ho of the two populations were 0.211 1 and 0.206 8, respectively. The genetic differentiation coefficient (Fst) was 0.005; In the cluster analysis of Structure model, the two populations were always clustered into one group and no individuals were isolated, which indicated that there was no significant genetic differentiation between the two populations of Luyuan chicken (P0.05). The number of inbred lines of the two populations was 0.178 8 and 0.193 5, respectively. The relatively high inbreeding level may be due to the small size of the initial basic group (rescue protection). Further selection signal analysis showed that the two populations of Luyuan chicken had some differentiation on chromosomal regions (loci), such as the chromosome region (loci), and 58 selected regions were identified by F- (st) and 胃 _ 蟺 test. GO and KEGG analysis showed that these differentially expressed genes were mainly concentrated in energy metabolism, signal transduction, stress immune response and other regulatory pathways. The whole genome SNP markers can be used to evaluate the status quo of species conservation more comprehensively. The results provide a basis for further optimization of breeding conservation techniques of Luyuan chicken.
【作者單位】： 江蘇省家禽科學(xué)研究所國家級地方雞種基因庫;張家港市畜禽有限公司;
【基金】：揚(yáng)州市自然科學(xué)基金項(xiàng)目(YZ2016134) 揚(yáng)州市高效農(nóng)業(yè)項(xiàng)目(YZ2016051)
【分類號】：S831.2

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