Recombination within the Cepaea nemoralis supergene is confounded by incomplete penetrance and epistasis

Although the land snail Cepaea nemoralis is one of the most thoroughly investigated colour polymorphic species, there have been few recent studies on the inheritance of the shell traits. Previously, it has been shown that the shell polymorphism is controlled by a series of nine or more loci, of which five make a single ‘supergene’ containing tightly linked colour and banding loci and more loosely linked pigmentation, spread band and punctate loci. However, one limitation of earlier work was that putative instances of recombination between loci within the supergene were not easily verified. We therefore generated a new set of C. nemoralis crosses that segregate for colour, banding and pigmentation, and several other unlinked shell phenotype loci. The snails were genotyped using a set of RAD-seq loci that flank the supergene, and instances of recombination tested by comparing inferred supergene genotype against RAD-marker genotype. We found no evidence that suspected ‘recombinant’ individuals are recombinant within the supergene - point estimates of recombination between both colour/banding, and colour/pigmentation loci are zero, with upper limits of 0.8 and 1.8%. Incomplete penetrance and epistasis are a better explanation for the apparent ‘recombinant’ phenotypes. Overall, this work therefore provides a resource for fine mapping of the supergene and other major shell phenotype loci. It also shows that the architecture of the supergene may not be as previously supposed.

Application of Marker-assisted Selection in Persimmon Breeding of PCNA Offspring Using SCAR Markers among the Population from the Cross between Non-PCNA ‘Taigetsu’ and PCNA ‘Kanshu’

Persimmon (Diospyros kaki Thunb) is hexaploid, and the pollination-constant, non-astringent (PCNA)/non-PCNA trait of Japanese origin is qualitatively controlled by the AST/ast alleles at a single locus and the PCNA trait is recessive to the non-PCNA trait. To avoid inbreeding depression led by repeated crosses among PCNA genotypes, non-PCNA genotypes should be used as cross parents. The marker-assisted selection system has been developed for the selection of PCNA offspring in the progeny derived from the cross of non-PCNA ‘Taigetsu’ (non-PCNA ‘Kurokuma’ × PCNA ‘Taishu’) to PCNA ‘Kanshu’. The primer pairs E8.5/E9r and 7H9F/AST-R were used for detecting the molecular markers A1 and A3, respectively, which link AST alleles. Complete agreement was found between the sequence-characterized amplified region (SCAR) marker genotype and fruit astringency phenotype of the 48 offspring. The result confirmed that the marker-assisted selection using those markers was highly practical. In a larger offspring population (522 offspring) from the same cross, offspring segregated into 100 with both markers, 162 with only A1, 179 with A3, and 81 with neither, and this segregation ratio was significantly different from 2:3:3:2, which is the segregation ratio of random chromosome assortment in autohexaploid. The percentage of offspring expected to be PCNA was 15.5% (81 of 522), which was slightly lower than 20%.

Effectiveness of selective genotyping for detection of quantitative trait loci: an analysis of grain and malt quality traits in three barley populations

Marker genotype data and grain and malt quality phenotype data from three barley (Hordeum vulgare L.) mapping populations were used to investigate the feasibility of selective genotyping for detection of quantitative trait loci (QTLs). With selective genotyping, only individuals with high and low phenotypic values for the trait of interest are genotyped. Here, genotyping of 10 to 70% of each population (i.e., 5 to 35% in each tail of the phenotypic distribution) was considered. Genomic positions detected by selective genotyping were compared to QTL position estimates from interval mapping analysis using marker genotype data from the entire population. Selective genotyping reliably detected almost all of the mapped QTLs, often with only 10% of the population genotyped. Selective genotyping also detected spurious QTLs in regions of the genome where no significant QTL had been mapped. Even with additional genotyping to verify putative QTLs, the total genotyping effort for detection of QTLs for a single trait by selective genotyping was usually less than 30% of that required for conventional interval mapping. Simultaneous investigation of two or more traits by selective genotyping would require additional genotyping effort, but could still be worthwhile.Key words: selective genotyping, quantitative trait loci, barley.

Investigating the Probability of Sign Inconsistency in the Regression Coefficients of Markers Flanking Quantitative Trait Loci

Estimates of the locations and effects of quantitative trait loci (QTL) can be obtained by regressing phenotype on marker genotype. Under certain basic conditions, the signs of regression coefficients flanking QTL must be the same. There is no guarantee, however, that the signs of the regression coefficient estimates will be the same. We use sign inconsistency to describe the situation in which there is disagreement between the signs of the estimated regression coefficients flanking QTL. The presence of sign inconsistency can undermine the effectiveness of QTL mapping strategies that presume intervals whose markers have regression coefficient estimates of differing sign to be devoid of QTL. This article investigates the likelihood of sign inconsistency under various conditions. We derive an analytic expression for the approximate probability of sign inconsistency in the single-QTL case. We also examine sign inconsistency probabilities when multiple QTL are present through simulation. We have discovered that the probability of sign inconsistency can be unacceptably high, even when the conditions for QTL detection are otherwise quite favorable.

Marker controlled inheritance of the polled locus in Simmental cattle

The inheritance of the polled phenotype in Simmental cattle was tested for linkage with alleles of four microsatellite markers on the proximal region of BTA1. For the study half-sib offspring of three sires were selected which are known to be heterozygous for the polled condition. The analysis of 57 animals (42 polled and 15 horned) revealed complete linkage between the polled locus and the markers BM6438 and SODlMicro2. The reliability of the prediction of the hörn Status of the offspring for marker assisted selection was estimated from its marker genotype in comparison to the patemal haplotype phases responsible for polledness, and from the allele frequencies of the favoured marker alleles in the random population.