畜牧学硕士毕业论文：本研究测定了11个家鸡（3个巴布亚新几内亚的地方群体、5个中国地方群体和3个商业品种）和1个红原鸡群体在20个常染色体微卫星座位上的遗传多样性；统计了观察等位基因频率（Na）、有效等位基因数(Ne)、杂合度(H)和多态信息含量(PIC)等遗传多样性参数；依据Nei’s DS和DA遗传距离，采用UPGMA法和NJ法构建了分子系统聚类树；并用STRUCTURE软件推导了群体的遗传结构。结果表明：20个微卫星座位均表现高度多态，在588个样品中共拥有213个等位基因，其中检测到等位基因数最多的座位是LEI0234，为27个；最少的是MCW0222，只有5个；每个基因座上的平均Na为10.65 ± 5.30，平均Ne2.954 ± 0.089，平均PIC为0.526 – 0.680，除LEI0166、MCW0216、MCW0248、MCW0222、MCW0014、MCW0067和MCW0081等七个基因座的PIC在0.4 – 0.5之间外，其余座位的PIC均大于0.5；除座位MCW0216外，其它座位在1至6个群体中显著地偏离Hardy-Weinberg平衡（P < 0.05），而各群体则在1至12个基因座上显著地偏离Hardy-Weinberg平衡（P < 0.05）。
12个群体的遗传多样性较为丰富，平均期望杂合度为0.615，其中最高的是巴布亚新几内亚的PMA群体，为0.680，最低的是罗曼鸡，为0.526。AMOVA分析表明红原鸡与所有家鸡品种以及商业品系与地方鸡品种的遗传变异水平相当，而中国地方鸡品种和巴布亚新几内亚地方鸡品种间的差异从整体上看是相对较小的。
各个群体间的Nei’s DS和DA的变化趋势基本一致，海南红原鸡与所有家鸡群体间的遗传距离都较远，其中与罗曼鸡之间的遗传距离最远（DA = 0.460）；海兰褐和罗曼鸡之间的遗传距离最近（DA = 0.064）。聚类分析、主成分分析和群体遗传结构推导均表明群体间的遗传背景差异较大，12个群体可以分为7类：蛋用商业品系的海兰褐和罗曼鸡；肉用商业品系爱拨益加鸡；甘肃的两个地方群体 - 会宁鸡和民勤鸡；福建的地方群体 - 德化黑鸡；经过选育的地方群体 - 北京油鸡和福建丝羽无骨鸡；巴布亚新几内亚的三个地方群体；海南红原鸡。
关键词：鸡；地方品种；商业品系；红原鸡；微卫星；遗传多样性
Abstract
Genetic diversity within and differentiation among 11 chicken breeds (three indigenous chicken populations from Papua New Guinea, five indigenous chicken populations from China and three commercial breeds also sampled in China) and one red juglefowl population from Hainan, China were assessed using 20 autosome microsatellite DNA loci. Allele frequency, number of observed alleles (Na), number of effective alleles (Ne), heterozygosity (H), and polymorphic information content (PIC) were calculated among other genetic diversity parameters. NJ and UPGMA phylogenetic trees were reconstructed using Nei’s DS and DA genetic distances. The genetic structure of these populations was further estimated using principal component analysis and STRUCTURE program. Some results and conclusions are made as follows:A total of 213 alleles were detected in 588 samples of the 12 populations, of which loci of LEI0094 and LEI0234 had the highest Na of 21 and 27, respectively, while locus of MCW0222 had five alleles. The estimates of average Na, Ne and PIC per locus among the 12 populations were 10.65 ± 5.30, 2.954 ± 0.089 and 0.526 - 0.680, respectively. Except for loci of LEI0166, MCW0216, MCW0248, MCW0222, MCW0014, MCW0067 and MCW0081 with PIC values ranging from 0.4 to 0.5, the PIC values of remaining loci were larger than 0.5. Apart from locus of MCW0216, http://www.51lunwen.org/xumu/ the rest of the 19 loci deviated significantly from the Hardy-Weinberg equilibrium in one to six populations (P < 0.05). Among the populations, there were 1 to 12 loci deviated significantly from the Hardy-Weinberg equilibrium in one to 12 populations (P < 0.05).
Genetic diversity was high in all 12 populations with estimates of average expected heterozygosity (He) per population of 0.615. The highest He was 0.680 in the PMA population of Papua New Guinea while the lowest He was 0.526 in the Lohmann Brown. AMOVA analysis showed that the levels of genetic variations between the red junglefowl and all domestic chicken populations, and between the commercial breeds and indigenous chicken populations were equivalent, while the indigenous chickens from China and Papua New Guinea had a relatively low genetic differentiation.
The patterns of Nei’s DS and DA genetic distances between the populations were similar. The red jungle population had the most distant genetic distances from all chicken populations with the highest DA estimate of 0.460 between the red junglefowl and the Lohmann Brown while Hy-line Brown and Lohmann Brown had the closest DA genetic distance of 0.064. Clustering and principal component analyses and population genetic structure estimates revealed seven groups among the 12 populations: Hy-line Brown and Lohmann Brown; Arbor Acres broiler; Huining and Minqin populations in Gansu, China; Dehua Black in Fujiang, China; Beijing Fatty and Silkie in Fujian, China; PMA, PAL and PPO chickens in Papua New Guina; red junglefowls.
Key words: chicken, indigenous breed, comme
