Real-time PCR genotyping assay for feline erythrocyte pyruvate kinase deficiency and mutant allele frequency in purebred cats in Japan

Erythrocyte pyruvate kinase (PK) deficiency is an inherited glycolytic erythroenzymopathy caused by mutations of the PKLR gene. A causative mutation of the feline PKLR gene was originally identified in Abyssinian and Somali cats in the U.S.A. In the present study, a TaqMan probe-based real-time PCR genotyping assay was developed and evaluated for rapid genotyping and large-scale screening for this mutation. Furthermore, a genotyping survey was carried out in a population of four popular purebred cats in Japan to determine the current mutant allele frequency. The assay clearly displayed all genotypes of feline PK deficiency, indicating its suitability for large-scale survey as well as diagnosis. The survey demonstrated that the mutant allele frequency in Abyssinian and Somali cats was high enough to warrant measures to control and prevent the disease. The mutant allele frequency was relatively low in Bengal and American Shorthair cats; however, the testing should still be carried out to prevent the spread of the disease. In addition, PK deficiency should always be considered in the differential diagnosis of anemia in purebred cats in Japan as well as worldwide.     

Identification of the putative ancestral allele of bovine single‐nucleotide polymorphisms

Identifying the action of natural selection from patterns of standing genetic variation has long been of interest to the population genetic community. Thanks to the availability of large single‐nucleotide polymorphism (SNP) data sets for many species and of high‐throughput SNP genotyping methods, whole‐genomic surveys to detect selective sweeps are now possible. Knowing the ancestral allele increases the power to detect selection. We present here a comparative genomic approach to determine the putative ancestral allele of bovine SNPs deposited in public databases. We analysed 19 551 488 SNPs and identified the putative ancestral allele for 14 339 107 SNPs. Our predicted ancestral alleles were in agreement with ancestral alleles detected by genotyping outgroup species for 97% SNPs from the BovineSNP50 BeadChip. This comparison indicates that our comparative genomic‐based approach to identify putative ancestral alleles is reliable.     

西林水牛群体的RAPD遗传多样性分析

【目的】了解西林水牛群体的遗传变异和遗传结构,为其辅助标记育种、遗传资源保护及利用提供参考依据。【方法】从广西西林县的8个乡（镇）采集184份西林水牛血样,采用优化后的RAPD技术检测其多态性DNA,统计多态性条带数,并应用Popgene32软件对西林水牛群体的有效等位基因数、Nei氏基因多样性指数及Shannon多样性指数进行分析。【结果】从18条RAPD引物中筛选出8条扩增产物稳定、条带清晰可辨的引物,扩增出的DNA片段分子量为100-1000 bp;从184个样本中共扩增出4968个多态性条带,平均每条引物可扩增出621个多态性条带,多态性频率达60.0%-100.0%,平均为89.7%。西林水牛群体的平均有效等位基因数为1.6745,平均Nei氏基因多样度指数为0.3583,平均Shannon多样性指数为0.5510。【结论】西林水牛群体的遗传变异、遗传分化及遗传多样性均较高,但选育程度较低,育种潜力较大,有待进一步保种和开发利用。     

Allele Types of Rc Gene of Weedy Rice from Jiangsu Province,China

Weedy rice(Oryza sativa f. spontanea), the predominant type of which has a red pericarp, seriously inhibits growth and yield of direct-seeded rice in Jiangsu Province, China. In this study, we randomly selected 10 weedy rice accessions from 10 plots in Jiangsu, and then sequenced the full lengths of their Rc genes(approximately 6.4 kb). In addition, we collected 166 different full-length Rc genes in the Oryza genus from the literature and from GenBank. A collinearity sequence analysis showed that the 10 weedy rice accessions from Jiangsu all had the same wild-type allele of the Rc gene. Single nucleotide polymorphisms indicated that the nucleotide polymorphisms(π = 0.19) and the proportion of segregation sites(θw = 0.28) of the Rc genes in the 10 weedy rice accessions from Jiangsu were higher than those in 56 weedy rice accessions from USA(π = 0.09 and θw = 0.07). Haplotype and phylogenetic analyses showed that the Rc genes of weedy rice accessions from Jiangsu were not revertants of the rc gene found in Asian cultivated rice(O. sativa) varieties with white pericarp. In addition, Rc gene sequences of the rice varieties Lvdao from Lianyungang, Jiangsu and Tangdao from Anhui were more similar to those of cultivated rice than to the weedy rice from Jiangsu. These findings support the continued quarantine of weedy rice and clarify the evolutionary mechanism of the red pericarp found in the weedy rice of Jiangsu.     

甜玉米LCYE等位基因多态性及功能分析

【目的】鉴定甜玉米材料中LCYE基因的多态性和β-胡萝卜素和类胡萝卜素含量的变异,为了解甜玉米LCYE基因的等位基因功能及维生素A源强化育种提供参考和依据.【方法】以47份甜玉米自交系为材料,用高效液相色谱法检测β-胡萝卜素和总类胡萝卜素的含量,扩增LCYE基因并测序,结合LCYE基因的测序结果和β-胡萝卜素、总类胡萝卜素含量的表型值作关联分析.【结果和结论】在47份甜玉米自交系的LCYE基因的测序结果中共发现75个多态性位点,其中49个多态性位点分布在非编码区,26个多态性位点分布于LCYE基因的外显子区,且均为SNP,第5外显子区多态性位点最丰富,第4和第9外显子区未检测到多态性位点,其保守程度较高.关联分析检测到与β-胡萝卜素相关联的位点3个,与总类胡萝卜素含量关联的位点6个,位点exon1-2和exon5-6与2种表型极显著相关.本研究证明在甜玉米中LCYE基因与β-胡萝卜素和类胡萝卜素的合成显著相关,为甜玉米的维生素A源强化育种提供了理论基础.     

湟中马血清酯酶多态性的研究

采用聚丙烯酰胺凝胶电泳法对青海省湟中县９１匹马血清酯酶的多态性进行了研究。结果发现：①湟中马的血清酯酶受ＥＳ＾Ｆ，ＥＳ＾Ｉ，ＥＳ＾Ｓ和ＥＳ＾Ｏ４个等位基因的控制，其基因频率分别为０．４４５０，０．５３３０，０．０１１０和０．０１１０；②在被检湟中马的ＥＳ位点上共发现ＥＳ Ｆ，ＥＳ ＦＩ，ＥＳ Ｉ，ＥＳ ＩＳ和ＥＳ Ｏ五种表型，以ＥＳ ＦＩ为优势表型（４７．２５％）；③ＥＳ等位基因频率无性别差异；④     

Gene dropping analysis of founder contributions in a closed Japanese black cattle population

Gene dropping simulation was applied to Japanese Black cattle population in Hyogo prefecture, to examine the survivals of alleles originated from founder animals. In the analysis, unique alleles were assigned to founders, and the genotypes of all descendants along the actual pedigree were generated through Monte Carlo simulation following Mendelian segregation rules. By replicating this process 10 000 times, the distribution of frequencies of alleles from each founder was estimated. From the distribution, several quantities useful for the management of genetic diversity, such as the probability of allele extinction and the probability of alleles surviving at a critically low frequency were derived. The materials used were 68 781 animals born in 1955–1998 and their pedigree records traced back to the population in 1937 or before. The expected number of alleles retained in the population drastically decreased during the analyzed period, and reached to 57.9 in the population of 1998, which was only 3.3% of the total number of alleles assigned to founders. Detailed analysis of major founders with relatively high genetic contributions to the current population revealed that alleles from most of the major founders are now at high risk of future extinction. These results strongly suggest that for the management of genetic diversity, the genetic contributions of founders are not fully informative, and emphasize the importance of the detection of live animals having founder alleles with high extinction possibilities.     

2··, a new high molecular weight glutenin subunit coded by Glu-A1: its predicted structure and its impact on bread-making quality

The suitability of wheat varieties for bread‐making depends on their glutenin subunits. The amino acid composition of these gluten building‐blocks have a strong influence on the rheology of the dough and, thus, on the suitability of the variety for bread‐making. This study reports a new x‐type high molecular weight glutenin subunit coded by the locus Glu‐A1 and named 2··. To investigate the impact of this allele on 10 quality parameters, a doubled haploid (DH) population of Triticum aestivum, segregating for Glu‐A1, was created. The statistical analysis demonstrates that, at Glu‐A1, the subunit 2·· is as favourable for quality as the subunit 2*. This is in accordance with results showing that the 2·· open reading frame still has the same number of cysteines as 2*. The small differences in the length of the central domain had no detectable effect on the elasticity, tenacity and baking quality, of the dough.