紫花苜蓿QTL与全基因组选择研究进展及其应用

四倍体紫花苜蓿是重要的豆科牧草之一,由于其复杂的遗传背景与二倍体作物相比遗传作图与重要性状数量性状位点(quantitative trait locus,QTL)定位研究相对滞后。然而,二倍体苜蓿的相关研究起步较早,已经建立了高密度遗传图谱和物理图谱,这些研究为四倍体苜蓿遗传作图与QTL定位奠定了基础。随着第三代分子标记与测序技术的快速发展,极大地促进了四倍体苜蓿的高密度遗传图谱构建与QTL定位研究,并借助分子标记辅助育种技术对提高苜蓿选育效率,加速育种进程具有重要意义。本文对苜蓿遗传图谱构建与QTL定位研究及发展趋势进行了总结,并对苜蓿关联作图与全基因组选择的研究进展及应用前景加以概述,旨在为读者就相关研究领域有较全面的了解。     

Accounting for heterogeneity of variances to improve the precision of QTL mapping in dairy cattle

The principle of interval mapping for quantitative trait loci (QTL) was originally developed for the analysis of single backcross data but it has been increasingly applied to more complicated experimental designs and data structures. It is important to study whether accounting for the heterogeneity of variance would improve the precision of QTL mapping based on data of multiple populations or families. This study compared homogeneous and heterogeneous maximum likelihood approaches for QTL mapping. The data consisted of 433 sons from six sire families with 69 microsatellite markers distributed over 12 chromosomes. The results of this study indicate that the heterogeneous approach generally produced a smaller residual variance and thus provided a better fit to the data than the homogeneous approach, meaning that the heterogeneous approach offers better precision in estimating both positions and effects of QTL. The results further showed that accounting for the heterogeneity of residual variance led to different statistical inferences from ignoring the heterogeneity of variance in QTL mapping. The heterogeneous approach is useful for QTL mapping based on the joint data of diverse reference populations or heteroscedastic data obtained from crossing animals with different genetic backgrounds.     

Fine mapping of a quantitative trait locus on chromosome 9 affecting non-return rate in Swedish dairy cattle

We previously mapped a quantitative trait locus (QTL) affecting the trait non-return rate at 56 days in heifers to bovine chromosome 9. The purpose of this study was to confirm and refine the position of the QTL by using a denser marker map and fine mapping methods. Five families that previously showed segregation for the QTL were included in the study. The mapping population consisted of 139 bulls in a granddaughter design. All bulls were genotyped for 25 microsatellite markers surrounding the QTL on chromosome 9. We also analysed the correlated trait number of inseminations per service period in heifers. Both traits describe the heifer's ability to become pregnant after insemination. Linkage analysis, linkage disequilibrium and combined linkage and linkage disequilibrium analysis were used to analyse the data. Analysis of the families jointly by linkage analysis resulted in a significant but broad QTL peak for non-return rate. Results from the combined analysis gave a sharp QTL peak with a well-defined maximum in between markers BMS1724 and BM7209, at the same position as where the highest peak from the linkage disequilibrium analysis was found. One of the sire families segregated clearly at this position and the difference in effects between the two sire haplotypes was 2.9 percentage units in non-return rate. No significant results were found for the number of inseminations in the combined analysis.     

Mapping the quantitative trait loci (QTL) for body shape and conformation measurements on BTA1 in Japanese Black cattle

The detection and mapping of segregating quantitative trait loci (QTL) that influence withers height, hip height, hip width, body length, chest width, chest depth, shoulder width, lumbar width, thurl width, pin bone width, rump length, cannon circumference, chest girth, abdominal width and abdominal girth at weaning was conducted on chromosomal regions of bovine chromosome one. The QTL analysis was performed by genotyping half‐sib progeny of five Japanese Black sires using microsatellite DNA markers. Probability coefficients of inheriting allele 1 or 2 from the sire at specific chromosomal locations were computed. The phenotypic data of progeny were regressed on these probability coefficients in a within‐common‐parent regression analysis using a linear model that included fixed effects of sex, parity and season of birth, as well as age as a covariate. F‐statistics were calculated every 1 cM on a linkage map. Permutation tests of 10 000 iterations were conducted to obtain chromosome‐wide significance thresholds. A significant QTL for chest width was detected at 91 cM in family 3. The detection of this QTL boosts the prospects of implementing marker‐assisted selection for body conformation traits in Japanese Black beef cattle.