Admixture analyses and phylogeographic relationships reveal complete genetic distinctiveness of Polish farm and wild red foxes (Vulpes vulpes) and the North American origin of farm‐bred individuals

A number of studies showed that many mtDNA haplotypes were shared among contemporary farm red foxes bred on different continents and the historical wild red foxes of North American origin. Therefore, in this study, the population genetic structure and phylogeographic relationships of Polish red foxes kept on fur farms and their wild conspecifics were investigated to assess the ancestry of the farm red foxes in Poland. A total of 330 tissue samples (200 from farm foxes and 130 from wild foxes) were used for the genetic analyses. Thirty microsatellite loci and two regions of mtDNA were used to assess the level of admixture between farm‐ and wild red foxes, to construct haplotype networks and create a phylogenetic tree. The genetic structure analysis clearly indicated two genetic clusters as being the most probable number of genetically distinct populations. The fixation index revealed a significant genetic distance between the farm‐ and wild red fox populations (F_ST = 0.27, p < 0.05). Haplotype networks based on frequencies showing relationships between concatenated haplotypes of Polish farm‐ and wild red foxes and the constructed phylogenetic tree clearly indicated two genetically distinct groups. The results of this study provide strong evidence confirming the North American origin of red foxes bred on Polish farms and the genetic distinctiveness of both studied populations.     

The primary gene pool of cassava (Manihot esculenta Crantz subspecies esculenta, Euphorbiaceae)

The primary gene pool (GP-1) of a crop is composed of gene reservoirs that cross easily with the domesticated, while the crosses regularly produce fertile offspring. The GP-1 is further subdivided into cultivated and wild gene pools. The cultivated gene pool encompasses commercial stocks of the crop, as well as landraces. The wild GP-1 of the crop comprises putative ancestors and closely related species that show a fair degree of fertile relationships with the domesticate. Two South American wild subspecies of cassava (M. flabellifolia and M. peruviana) were proposed as natural members of the wild GP-1 of the crop. Another Brazilian species(M. pruinosa) is morphologically so close to both wild subspecies that it may turn out as another member of the wild GP-1. This revised version was published online in July 2006 with corrections to the Cover Date.     

Whole-genome resequencing reveals diversity,global and local ancestry proportions in Yunling cattle

Yunling cattle, a three-breed cross consisting of 1/2 Brahman cattle, 1/4 Murray Grey cattle and 1/4 Yunnan Yellow cattle, has advantage of rapid growth, good meat quality, enhanced tolerance towards a hot and humid climate, tick resistance and crude feed forbearance. Here, we investigated the genetic diversity, global and local ancestry proportions by sequencing the genomes of 131 Yungling cattle and 31 Brahman cattle (for control). Furthermore, we used 35 published genomes of ancestry breeds (including Angus cattle [ancestry of Murray Grey], Wannan cattle [ancestry of Yunnan Yellow cattle: Wenshan and Dianzhong], Wenshan and Dianzhong cattle) to characterize the formation process of Yunling cattle. The highest nucleotide diversity was found in the Wannan cattle, followed by Wenshan, Dianzhong, Brahman, Yunling and Angus cattle. The results of LD decay in each breed was largely consistent with the results of nucleotide diversity, except for the faster decay in Angus cattle out of a smaller effective population size and a strong bottleneck during the breed formation. The population-structure analysis revealed that the cross-breed Yunling cattle harboured the ancestry with Angus (0.44), Brahman (0.48) and Wannan cattle (0.08). Subsequently, we used RFmix to infer local ancestry in Yunling cattle and then performed chi-squared test to obtain the segments whose proportions of a certain ancestry were excessive compared with the whole-genome level, leading to 391 Angus, 49 Brahman and 2,312 Wannan segments. Gene annotation and KEGG enrichment analysis revealed that the excessive Angus, Brahman and Wannan segments might contribute to the rapid growth, immune resistance and indigenous adaptation, respectively, in Yunling cattle. Our results help understand ancestry components and formation process in Yunling cattle and will provide an opportunity for selective breeding by molecular approaches in future.     

中国大豆育成品种的亲本分析

中国１９２３～１９９２年间育成的５６４个大豆品种可追溯到３０８个祖先亲本，其中２３０个为地方品种，３９个为主要来自美国的引种，其余３９个为遗传基础不详的国内育种品系。从中分别评出东北、黄淮海、南方三大主产区育成品种的主要祖先亲本１０，１０，７份，另有国外引种１０份，共计３７份。由３０８个祖先亲本构成的３０８个系谱树中，５个衍生有５０个以上的育成品种，最多的为金元，共衍生有７轮２０８个品种。近１２年育成品种的亲本中１６％为地方品种，３９％为育成品种，３２％为育种品系，１３％为国外引种。三大主产区间育种亲本相互引用呈上升趋势。