Admixture analysis in relation to pedigree studies of introgression in a minority British cattle breed: the Lincoln Red

Investigation of historic population processes using molecular data has been facilitated by the use of approximate Bayesian computation (ABC), which enables the consideration of multiple alternative demographic scenarios. The Lincoln Red cattle breed provides a relatively simple example of two well‐documented admixture events. Using molecular data for this breed, we found that structure did not resolve very low (<5% levels) of introgression, possibly due to sampling limitations. We evaluated the performance of two ABC approaches (2BAD and DIYABC) against those of two earlier methodologies, ADMIX and LEADMIX, by comparing their interpretations with the conclusions drawn from herdbook analysis. The ABC methods gave credible values for the proportions of the Lincoln Red genotype that are attributable to Aberdeen Angus and Limousin, although estimates of effective population size and event timing were not realistic. We suggest ABC methods are a valuable supplement to pedigree‐based studies but that the accuracy of admixture determination is likely to diminish with increasing complexity of the admixture scenario.     

LDSO: a program to simulate pedigrees and molecular information under various evolutionary forces

Simulations are a major tool to evaluate new statistical methods and optimize experimental designs in the genomic era. However, this can only be achieved when the simulations are close enough to reality, as well as diverse enough to be realistic. For mapping studies, it is thus critical to re-create as much as possible the forces generating linkage (mutation, random drift, changes in population sizes, selection and pedigree structure) and the mechanisms producing trait genetic architecture (additivity, dominance, epistasis). We present here a computer program (ldso) simulating these phenomena. Optional outputs provide statistics on the linkage disequilibrium (LD) structure and the identity by descent between chromosomal segments, facilitating further data analyses. Furthermore, ldso enables the simulation of genomic data in known pedigrees, which sticks as precisely as possible to recent population history and structures of the long-range LD, allowing optimization of fine-mapping strategies.     

Comparison of Spring Barley Lines Produced by Single Seed Descent, Pedigree Inbreeding and Doubled Haploidy

Samples of inbred lines of Hordeum vulgare produced by pedigree inbreeding, doubled haploidy and single seed descent have been compared for a range of agronomic characters. Differences between the means of the in bred s produced by single seed descent and pedigree breeding were due to differing levels of inbreeding. The present study confirmed chat recombinant inbred families which out-perform the higher scoring parent may be produced by either method. Caution should, however, be exercised when simply inherited characters controlled by major genes are fixed in early generations. Differences between the doubled haploid and single seed descent samples for the character thousand grain weight were attributable to coupling linkages involving epistatic genes. The production and evaluation of random inbred lines should be considered as an alternative to pedigree methods of barley breeding.     

Parentage assignment in Haliotis midae L.: a precursor to future genetic enhancement programmes for South African abalone

The establishment and evaluation of family lines using pedigree information provides an advanced understanding of the variability that exists for complex, economically valuable traits and is a necessary step in the execution of an effective breeding programme. The aim of this study was to assign parentage to mass‐spawned Haliotis midae juveniles using species‐specific microsatellite markers. Screening of wild abalone individuals revealed that the nine loci selected complied with the minimum requirements for parentage analyses: a null allele frequency <5% as well as a high number and frequency of alleles per locus. A total of 598 individuals were genotyped (198 breeding individuals and 400 F1 progeny) from two farms, with parentage results yielding 91% and 90% successful assignment for Farms A and B respectively. This study, therefore, provided the necessary pedigree information required for controlled breeding of individual adult abalone and indicated the usefulness of the panel of microsatellite markers selected for parentage assignment.     

大骨鸡快慢羽群体系谱完整性分析

利用系谱完整性指数(Pedigree Completeness Index,PCI)统计分析辽宁庄河大骨鸡快慢羽群体系谱的完整情况。结果显示,庄河大骨鸡的系谱完整性较好(PCI为0.92±0.18);对于系谱的完整性,快羽群体(PCI为0.88±0.23)与慢羽群体(PCI为0.94±0.15)之间不存在明显差异。     

黑龙江水稻育种骨干亲本及系谱分析

分析了黑龙江省审定的260个水稻品种的骨干亲本和20世纪90年代后育成品种的系谱.结果表明,20世纪90年代前育成品种的骨干亲本是石狩白毛、农林11号、虾夷,由它们育成或衍生品种占同期育成品种的83.3%,其中骨干核心亲本是石狩白毛,由它直接育成或衍生的品种数占同期育成品种总数的44.1%:20世纪90年代后育成品种的...     

Extensive dispersal of Roanoke logperch (Percina rex) inferred from genetic marker data

The dispersal ecology of most stream fishes is poorly characterised, complicating conservation efforts for these species. We used microsatellite DNA marker data to characterise dispersal patterns and effective population size (N_e) for a population of Roanoke logperch Percina rex, an endangered darter (Percidae). Juveniles and candidate parents were sampled for 2 years at sites throughout the Roanoke River watershed. Dispersal was inferred via genetic assignment tests (ATs), pedigree reconstruction (PR) and estimation of lifetime dispersal distance under a genetic isolation‐by‐distance model. Estimates of N_e varied from 105 to 1218 individuals, depending on the estimation method. Based on PR, polygamy was frequent in parents of both sexes, with individuals spawning with an average of 2.4 mates. The sample contained 61 half‐sibling pairs, but only one parent–offspring pair and no full‐sib pairs, which limited our ability to discriminate natal dispersal of juveniles from breeding dispersal of their parents between spawning events. Nonetheless, all methods indicated extensive dispersal. The AT indicated unrestricted dispersal among sites ≤15 km apart, while siblings inferred by the PR were captured an average of 14 km and up to 55 km apart. Model‐based estimates of median lifetime dispersal distance (6–24 km, depending on assumptions) bracketed AT and PR estimates, indicating that widely dispersed individuals do, on average, contribute to gene flow. Extensive dispersal of P. rex suggests that darters and other small benthic stream fishes may be unexpectedly mobile. Monitoring and management activities for such populations should encompass entire watersheds to fully capture population dynamics.     

河南省大豆审定品种系谱来源及性状分析

为明确河南省大豆审定品种亲缘关系,借鉴有益于育种效果的经验与技术,分析了河南省1985—2012年审定的74个大豆品种的系谱来源、主要农艺性状和经济性状特点。结果表明,河南省审定的大豆品种可明确113个原始亲本,产量与原始亲本数量成显著正相关。河南省大豆审定品种的主要农艺性状中,生育期稳定在106 d左右,株高因品种而异,变化较大;产量构成因素中,单株荚数总体呈增加趋势,百粒质量则相对变化较小。113份原始亲本中,来自河南省及周边省份的原始亲本占总数的50%以上,各审定品种之间血缘关系过于密切。河南省大豆品种合理的产量构成因素应该是:单株荚数48.6个左右,百粒质量17.55~21.80 g。     

阿夫及其衍生小麦品种（系）的SSR分析

为了研究小麦骨干亲本阿夫(Funo)遗传物质在其衍生品种(系)的传递规律,用247对SSR引物对阿夫和8个阿夫子一代衍生品种(系)的亲本进行分析,发现有3个标记Xwmc398 (178 bp, 151 bp)、Xgwm400(180 bp, 149 bp)和Xgwm268(191 bp)在阿夫上有稳定、清晰的特异带。以筛选的特异引物对5个阿夫系选品种和255个阿夫衍生品种(系)进行了SSR分析。结果表明,Xwmc398在5个系选品种中均有阿夫的特异带,而Xgwm400只在安选2号,Xgwm268只在扬麦1号具有阿夫特异带。Xwmc398在阿夫子一代至子六代衍生品种(系)中的遗传频率分别为52.8%、38.4%、16.7%、0.0%、0.0%和0.0%, 平均为32.2%;Xgwm400的相应遗传频率分别为32.1%、19.2%、41.7%、33.3%、20.0%和0.0%,平均为26.7%;Xgwm268的相应传递率分别为22.6%、34.4%、11.1%、12.1%、0.0%和0.0%,平均为24.7%。表明SSR位点Xwmc398、Xgwm400和Xgwm268在阿夫衍生品种(系)中有明显的传递。     

矮秆玉米自交系08H67-2的选育

以性状上相互互补又同为Reid种质的郑58和长A37的杂交种为基础材料,按严格自交的系圃法进行选系,在自交4代即将稳定时,用EMS化学诱变剂对其进行处理,引发变异,选育出了矮秆玉米自交系08H67-2。