Accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (Scophthalmus maximus)

Many estimators and algorithms have been developed to infer the genealogical relationships from molecular marker data when there is no pedigree information. Most pairwise methods provide estimates in a continuous range that needs to be converted into genealogical relationships (namely full-sibs, half-sibs and unrelated) if there is a previous knowledge of the population structure. Transformations are usually based on arbitrary thresholds, but the possibility of correcting the coancestry estimates via explicit pedigree reconstruction methods has been suggested. Using molecular data for ten highly polymorphic microsatellite loci on a population of turbot (Scophthalmus maximus) with a known genealogy, the behaviour of four pairwise marker-based coancestry estimators and the molecular coancestry has been evaluated. The population consisted on 138 families with 4 full-sib individuals each and one family with 8 full-sib individuals (up to 15 half-sib families were also present due to the sharing of parents between some of the full-sibs families). Our results suggested that transforming the pairwise estimators and the molecular coancestry to family relationships through the establishment of thresholds performs slightly better than the explicit pedigree reconstruction method, when accuracy is measured in a pairwise basis. However, if joint relationships between more than two individuals were tested at a time, the threshold methods led to a high percentage of incongruous triads of full-sib individuals, with Mendelian incompatibilities appearing in congruous full-sib families (more than 70% and 60% in our study, respectively). The explicit pedigree reconstruction approach, due to its nature, is free from such problems. Therefore, the pedigree reconstruction approach seems to be a valuable tool to provide a congruent and compatible pedigree when the pairwise marker-based coancestry matrices or the molecular coancestry need to be transformed.     

The coefficient of dominance is not (always) estimable with biallelic markers

The genetic relationship among individuals at one locus is characterized by nine coefficients of identity. The coefficients of inbreeding, coancestry and dominance (or fraternity) are just linear functions of them. Here, it is shown how they can be estimated using biallelic and triallelic markers using the method of moments, and comparisons are made with other methods based on molecular coancestry or molecular covariance. It is concluded that in the general case of dominance and inbreeding with biallelic markers, only the coefficients of inbreeding and coancestry can be estimated, but neither the single coefficients of identity nor the coefficient of dominance can be estimated. More than two alleles are required for a full estimation as illustrated with the triallelic situation.     

广西主要杂交大豆育成品种系谱分析

对1981—2005年间广西杂交育成的大豆品种及有代表性的杂交育成品系进行了亲本来源分析,并在此基础上,采用共祖先度方法分析了它们之间的亲缘关系。结果表明,这17个大豆品种(系)共涉及25个原始亲本,其中广西地方品种8个,外省品种14个,外国品种3个,平均每个品种含有2.9个原始亲本。大多数亲本只衍生一个品种,衍生品种最多的亲本为“靖西早黄豆”(7个),其次为“北京豆”(6个)、“平果豆”、“杂交混选”和“矮脚早”均为3个,“青仁乌”和“玉林大豆”均衍生2个品种。杂交方式以单交为主,17个杂交育成品种中,采用单交方式杂交选育的有16个,仅有1个为复合杂交育成。祖先度分析阐明了原始亲本和杂交育成品种之间的亲缘关系远近,可为育种提供参考。     

Relationship between genealogical and microsatellite information characterizing losses of genetic variability: Empirical evidence from the rare Xalda sheep breed

Preservation of rare genetic stocks requires continual monitoring of populations to avoid losses of genetic variability. Genetic variability can be described using genealogical and molecular parameters characterizing variation in allelic frequencies over time and providing interesting information on differentiation that occurred after the foundation of a conservation program. Here we analyze the pedigree of the rare Xalda sheep breed (1851 individuals) and the polymorphism of 14 microsatellites in 239 Xalda individuals. Individuals were assigned to a base population (BP) or 4 different cohorts (from C1 to C4) according to their pedigree information. Genetic parameters were computed at a genealogical and molecular level, namely inbreeding (F), observed (H_o) and expected (H_e) heterozygosity, individual coancestry coefficients (f and f_m), average relatedness (AR), mean molecular kinship (Mk), average number of allele per locus (A), effective number of ancestors (f_a), effective population size (N_e and N_e(m)) and founder genome equivalents (N_g and N_g(m)). In general, the computed parameters increased with pedigree depth from BP to C4, especially for the genealogical information and molecular coancestry-based parameters (f_m, Mk and N_g(m)). However, H_o and H_e showed the highest values for C1 and the molecular heterozygote deficiency within population (F_IS(m)) showed the lowest value for C1, thus indicating that loss of genetic variability occurs very soon after the implementation of conservation strategies. Although no genealogical or molecular parameters are sufficient by themselves for monitoring populations at the beginning of a conservation program, our data suggests that coancestry-based parameters may be better criteria than those of inbreeding or homozygosity because of the rapid and strong correlation established between f and f_(m). However, the obtaining of molecular information in well-established conservation programs could not be justified, at least in economic terms.     

大豆优异种质商7608育种价值分析

对商7608种质与其12个衍生品种间共祖先度的分析和配合力测定结果表明：该种质遗传基础丰富，农艺性状优良，抗病性强，配合力高，具有极高的利用价值。在黄淮夏大豆区有着广阔的利用前景。     

Genetic diversity loss due to selection for scrapie resistance in the rare Spanish Xalda sheep breed

The effect of selection for scrapie resistance on genetic variability in the rare Xalda sheep breed was studied. Pedigree information comprised 1851 animals (1444 alive) at the moment of sampling. A total of 304 reproductive (or selected for reproduction) Xalda individuals were sampled and genotyped for 14 microsatellites. Genetic variability was assessed using: gene diversity (1 − average kinship, GD), mean average relatedness (AR) and self-coancestry (c_i) at the genealogical level; and expected heterozygosity (H_e), molecular mean kinship (Mk), molecular self-coancestry (s_i) and rarefacted average number of alleles per locus (A) at the molecular level. Two breeding strategies were evaluated: a) use of only young rams with genotype ARR/ARR and young ewes with low to moderate risk (risk groups R1 to R3); b) breeding without selection for PrP genotypes. The major cause of losses of genetic variability in the Xalda breed is the drift that occurs when a new group of reproductive individuals is selected. The loss of genetic variability is small in females compared to the males, where it is considerable. However, losses at the molecular level for young females with respect to adult females were above 5%. Young male individuals also retained most of the genetic variability assessed in adult rams. Selection against susceptibility to scrapie produced additional losses of more than 2% for H_e and A when rYF individuals are considered. As regards males, the situation becomes critical because of the scant number of available ARR/ARR young rams. The consequences for the management of the Xalda breed are discussed.     

黄淮夏大豆优异种质郑77249的育种价值分析

对郑７７２４９种质与其２４个衍生新品种间共祖先度的分配和配合力测定结果表明,该种质遗传基础丰富,农艺性状优良,抗病性强,配合力高,具有极高的利用价值在黄淮夏大豆区有着广阔的利用前景。     

广西主要杂交大豆育成品种系谱分析

对1981~2005年间广西杂交育成的大豆品种及有代表性的杂交育成品系进行了亲本来源分析,并在此基础上,采用共祖先度方法分析了它们之间的亲缘关系。结果表明,这17个大豆品种（系）共涉及25个原始亲本,其中广西地方品种8个,外省品种14个,外国品种3个,平均每个品种含有2.9个原始亲本。大多数亲本只衍生一个品种,衍生品种最多的亲本为“靖西早黄豆”（7个）,其次为“北京豆”（6个）、“平果豆”、“杂交混选”和“矮脚早”均为3个,“青仁乌”和“玉林大豆”均衍生2个品种。杂交方式以单交为主,17个杂交育成品种中,采用单交方式杂交选育的有16个,仅有1个为复合杂交育成。祖先度分析阐明了原始亲本和杂交育成品种之间的亲缘关系远近,可为育种提供参考。     

小麦骨干亲本豫麦2号的育种价值分析

河南审定的183个小麦品种中有75个小麦品种含有豫麦2号的血缘,豫麦2号成为河南小麦育种利用率最高的骨干亲本.利用系谱资料对豫麦2号种质与其75个衍生品种的共祖先度进行了分析.结果表明:75个小麦品种与豫麦2号的共祖先度范围为0.0500～0.6250,累积的共祖先度为20.9041,占75个小麦品种的27.87%,占河南183个小麦品种的11.42%,豫麦2号具有极高的利用价值,豫麦2号及其衍生品种的利用还在继续.研究豫麦2号的育种价值,对于有效利用小麦种质资源,保持小麦品系的遗传多样性,恰当地选用杂交亲本,成功地创造出优良新基因型具有重要意义.     

小麦骨干亲本豫麦2号的育种价值分析

河南审定的183个小麦品种中有75个小麦品种含有豫麦2号的血缘,豫麦2号成为河南小麦育种利用率最高的骨干亲本。利用系谱资料对豫麦2号种质与其75个衍生品种的共祖先度进行了分析。结果表明：75个小麦品种与豫麦2号的共祖先度范围为0.0500～0.6250,累积的共祖先度为20.9041,占75个小麦品种的27.87%,占河南183个小麦品种的11.42%,豫麦2号具有极高的利用价值,豫麦2号及其衍生品种的利用还在继续。研究豫麦2号的育种价值,对于有效利用小麦种质资源,保持小麦品系的遗传多样性,恰当地选用杂交亲本,成功地创造出优良新基因型具有重要意义。