Single nucleotide polymorphisms of the KIT and KITLG genes in pigs

Here, we report the variability in the KIT tyrosine kinase receptor and its ligand KITLG genes by determining single nucleotide polymorphisms (SNPs) in 384 individuals including 11 pig breeds, two synthetic-line cross pigs, two cross breeds, and one Japanese wild boar. SNPs and indels within the coding sequence regions of KITLG and KIT and their 5'-flanking regions were detected by aligning sequences from eight pigs, and subsequently the SNPs were genotyped using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF-MS). Principal component analysis using allele frequencies in the SNP locus showed a distant relationship between Asian and Euro-American pig groups, except for Berkshire and Tokyo X breeds. These breeds were located within the mid-portion of the distribution in the first principal component. The Hampshire breed was distant from the other pig groups on the axis of the second principal component. Haplotype frequencies that were deduced using non-synonymous substitutions of the KIT gene revealed the uniqueness of Landrace, Large White, Middle White, and three-way cross pigs (LWD) and of the Hampshire breed. On the other hand, the haplotypes of KITLG and KIT detected in the Berkshire breed were prevalent in Asian pig groups. This tendency is different from that observed in other Euro-American pig breeds.     

Estimation of variance and genomic prediction using genotypes imputed from low‐density marker subsets for carcass traits in Japanese black cattle

The influence of genotype imputation using low‐density single nucleotide polymorphism (SNP) marker subsets on the genomic relationship matrix (G matrix), genetic variance explained, and genomic prediction (GP) was investigated for carcass weight and marbling score in Japanese Black fattened steers, using genotype data of approximately 40,000 SNPs. Genotypes were imputed using equally spaced SNP subsets of different densities. Two different linear models were used. The first (model 1) incorporated one G matrix, while the second (model 2) used two different G matrices constructed using the selected and remaining SNPs. When using model 1, the estimated additive genetic variance was always larger when using all SNPs obtained via genotype imputation than when using only equally spaced SNP subsets. The correlations between the genomic estimated breeding values obtained using genotype imputation with at least 3,000 SNPs and those using all available SNPs without imputation were higher than 0.99 for both traits. While additive genetic variance was likely to be partitioned with model 2, it did not enhance the accuracy of GP compared with model 1. These results indicate that genotype imputation using an equally spaced low‐density panel of an appropriate size can be used to produce a cost‐effective, valid GP.     

Production of asexual and sexual offspring in the triploid sexual planarian Dugesia ryukyuensis

Certain freshwater planarians reproduce asexually as well as sexually, and their chromosomal ploidies include polyploidy, aneuploidy and mixoploidy. Previously, we successfully performed an experiment in which a clonal population produced by asexual reproduction of the Dugesia ryukyuensis (OH strain) switched to the sexual mode of reproduction. Worms of this strain are triploid with a pericentric inversion on Chromosome 4. The worms were switched to sexual reproduction after being fed with sexually mature Bdellocephala brunnea, which is a sexually reproducing species. The resulting sexualized OH strain produced cocoons filled with several eggs. Two putative factors, Mendelian factor(s) and chromosomal control(s), have been proposed as determining the reproductive mode. The present study demonstrated that inbreeding of the resultant sexualized worms produced the following four types of offspring through sexual reproduction: diploid asexual worms, triploid asexual worms, diploid sexual worms and triploid sexual worms. The chromosomal mutation on Chromosome 4 was inherited by these offspring independent of their reproductive mode. These results provide two important pieces of information: (i) the putative genetic factor was not necessarily inherited in a Mendelian fashion; and (ii) the reproductive mode is not regulated by chromosomal changes such as polyploidy or chromosomal mutations. This suggests that asexuality in D. ryukyuensis is regulated by an unknown factor(s) other than a Mendelian factor or a chromosomal control.     

Providing an intelligible explanation to pet owners by using three-dimensional CT images: Use of clinical imaging for better informed consent

The purpose of the study reported here was to discuss the level of intelligibility of three-dimensional computed tomography (3D-CT) images of clinical patients for persons who are lacking veterinary knowledge. 143 undergraduate students were participated in this study. They were entirely unfamiliar with veterinary anatomy. A survey was conducted using the visual analog scale method with a focus on the level of intelligibility of the 3D-CT images compared to that of the two-dimensional CT images or radiographs. As a result, the mean value of the intelligibility of the 3D-CT image was 88.4 ± 17.8 points out of 100 points. In clinical cases, it is very difficult for pet owners lacking veterinary knowledge to understand the clinical status of their pets even with explanations using illustrations, radiographs, and transverse CT images. It is considered that better informed consent and patient satisfaction will be obtained provided veterinarians make an effort towards intelligible patient education by using 3D-CT images.     

Quantitative trait locus analysis for days-to-heading and morphological traits in an RIL population derived from an extremely late flowering F<Subscript>1</Subscript> hybrid of sorghum

The hybrid vigor typical of F₁ cultivars is used to boost biomass production of sorghum (Sorghum bicolor (L.) Moench). The high dry-matter yielding F₁ cultivar Kazetachi uniquely shows extremely late flowering and a long culm, and is greatly different from its parents. We investigated the genetic mechanisms underlying these phenotypes by quantitative trait locus (QTL) analysis of recombinant inbred lines derived from a male-fertile line and a restorer line and grown in 3 years. QTL analysis for six traits (days-to-heading, culm length, culm width, culm number, panicle length, panicle number) revealed that the unique phenotypes of the F₁ plants were controlled by the genetic combination of 12 or more QTLs detected in at least 2 years. Two putative QTLs for days-to-heading (qDH1 on SBI-01 and qDH6 on SBI-06) would strongly affect the other phenotypes because of their co-localization with QTLs for other traits, as supported by significant phenotypic correlations. These QTLs would be useful for understanding the association of plant type with biomass production in sorghum.     

Quantitative trait loci for whiteness of cooked rice detected in improved rice cultivars in Hokkaido

Improving the eating quality of cooked rice has been one of the most important objectives in rice breeding programs. Eating quality of cooked rice is a complex trait including several components, such as external appearance, taste, aroma, and texture. Therefore, dissection of these components followed by marker-assisted selection of detected QTL(s) may be a useful approach for achieving desirable eating quality in rice breeding. Whiteness of cooked rice (WCR) is an important factor related to the external appearance of cooked rice. WCR is known to be associated with the amylose and protein contents of the endosperm. However, the genetic basis of WCR remains unclear. In this study, we evaluated phenotypic variation in WCR among recently developed rice cultivars from Hokkaido, Japan. Then, we developed doubled haploid lines (DHLs) derived from a cross between two cultivars from Hokkaido, Joiku No. 462 (high WCR) and Jokei06214 (low WCR). Using the DHLs, we detected two QTLs for WCR, qWCR3 and qWCR11, on chromosomes 3 and 11, respectively. We also examined the dosage effect of the two QTLs based on both the categorized segregants in the DHLs and the relationship between the WCR phenotype and inheritance around the QTL regions in cultivars from Hokkaido.