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The dominant T allele for tawny pubescence is associated with chilling tolerance in soybean [Glycine max (L.) Merr.]. Yellow hilum cultivars with dominant I allele are preferred in Japan because of superior external seed appearance. The allelic combination of IITT darkens the entire seed coat, giving a dirty appearance to seeds. Previous studies revealed a quantitative trait locus (QTL) for seed coat discoloration in the vicinity of the I locus. This study was conducted to identify a candidate gene for this QTL. A breeding line 0734BW-1 (IITT) with severe discoloration had an inverted repeat of chalcone synthase 3 pseudogenes (pCHS3s), whereas the 5' copy of pCHS3 was replaced by a fragment of a DnaJ-like protein gene in a breeding line 0518BW-8 (IITT) showing slight discoloration. A marker discriminating this structural polymorphism was mapped at the peak of the QTL, suggesting that pCHS3s might be responsible for seed coat discoloration. The gene structure of 0518BW-8 was identical to that of a gray pubescent cultivar Toyoharuka (IItt) that is tolerant to seed coat browning induced by low temperatures. These results suggest that pCHS3s may control the intensity of seed coat discoloration in tawny pubescent cultivars (TT) and browning in gray pubescent cultivars (tt). Regardless of pubescence color, the allele may be useful for breeding cultivars producing seeds with acceptable external appearance in high-latitude regions where low temperatures frequently prevail. [ABSTRACT FROM AUTHOR]

To clarify the spatial distribution of masu salmon Oncorhynchus masou with incongruent genotypic and phenotypic sex, we compared the phenotypic sex determined by gonad analysis with the genotypic sex identified by a male-specific genetic marker, Growth hormone pseudogene (GHp), in 584 individuals inhabiting 23 rivers in Hokkaido, Japan. We found that the genotypic sex is different from the phenotypic sex for 39 individuals in 10 rivers. Among them, 35 individuals (89.7 %) were GHp + females phenotypically. The opposite feature was noted in the remaining four individuals (10.3 %). This study also revealed that GHp + phenotypic females are distributed mainly in the Sea of Japan, whereas GHp- phenotypic male tend to appear in the Sea of Okhotsk. In addition, there was a significant negative correlation between the distance from the Bishabetsu River, where frequency of GHp + phenotypic females was the highest, and the frequency of those individuals in each river. These results suggest that the distribution of masu salmon with incongruent genotypic and phenotypic sex would be related to the movement of individuals among the populations and regions. [ABSTRACT FROM AUTHOR]

This study compared the growth rates of female masu salmon Oncorhynchus masou, who possessed a male-specific gene marker, the growth hormone pseudogene (GHp), and normal females, as estimated from their scale growth. There was a difference between the growth rates of GHp-positive females and those of normal females of the same age during the ocean period, although their growth rates during the river period were similar. These results suggest that GHp-positive salmonid females exhibit male-like characteristics such as reduced feeding activity during the ocean period, which depresses their growth., (© 2014 The Fisheries Society of the British Isles.)

The genetic sex of mature masu salmon Oncorhynchus masou (212 males and 243 females) collected from three rivers located in the mid-western part of Hokkaido was determined using the male-specific genetic marker growth hormone pseudogene (GHp). A total of 72 phenotypic females were found to have GHp, whereas none of the phenotypic males lacked GHp. The occurrence of females with incongruence between genotypic and phenotypic sex varied with the river and reached the highest rate of 67%. In contrast, none of the phenotypic males were found to have a female genotype. Comparison of adult body size showed that females with GHp were significantly smaller than those without GHp. Moreover, comparison of secondary characteristics revealed that both upper jaw length and head length were greater in females with GHp than in those without GHp. These results suggest that genetic changes (e.g. transposition and mutation) may also affect morphological characteristics., (© 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.)

Genomic DNA from a panel of 41 healthy unrelated Japanese individuals was typed for the presence or absence of 16 KIR genes and pseudogenes. Only eight different KIR genotypes were found. Group A haplotypes outnumbered group B haplotypes in frequency by approximately 3:1, with individuals having two group A haplotypes accounting for 56% of the panel. The frequency of A haplotypes in the Japanese is higher than that observed in other populations. Flow cytometric comparison of KIR expression in 19 panel members showed considerable diversity in NK cell repertoire, which was also seen within the group of individuals having two A haplotypes. This diversity is likely due to allelic polymorphism in expressed genes of the A haplotype. In comparison to other populations, the Japanese appear less heterogeneous in KIR genotype as assessed by gene content.

About 20%-25% of Caucasian individuals are nonsecretors who fail to express soluble A, B, H, and Lewis b histo-blood group antigens in secretory organs and secretory fluids because of the absence of the Secretor gene (FUT2)-encoded alpha(1,2)-fucosyltransferase (Se enzyme) activity. Recently, the FUT2 and a pseudogene have been isolated, and an Se enzyme-deficient allele (se) caused by a nonsense mutation (G428A, se1) in Caucasians has also been reported. Although we were unable to find the se1 allele, we have found a missense mutation (A385T, se2) and two nonsense mutations (C571T, se3 and C628T, se4) in the Japanese Se enzyme-deficient alleles. In addition, we have found a fusion gene, which consisted of the 5'-region of the pseudogene and the 3'-region of the functional FUT2, as a Se enzyme-deficient allele (se5). The DNA sequence analysis of the fusion gene indicated that the crossover region corresponded to regions between bases 253 and 313 of the pseudogene and between bases 211 and 271 of the FUT2. This finding suggested that the fusion gene was generated by homologous but unequal crossover. A population study on 141 randomly selected Japanese has indicated that the se2 is a common Se enzyme-deficient allele in the Japanese population. The results suggest that Se enzyme-deficient alleles are race specific.

During the course of structural gene analysis of a family with type III protein S deficiency, we found a novel DNA polymorphism: an A or G variation at nucleotide 732 in exon 6 of the PS-alpha gene. This A to G mutation would lead to a substitution of Lys155 by Glu in the second EGF domain. Linkage study with restriction enzyme analysis using mutagenic PCR strategy showed that the same mutation was also present in three other members of the patient's family and two individuals from an unrelated kindred, while they all had normal amounts of both immunological and functional PS levels. Restriction enzyme analysis of 182 normal Japanese genomic samples showed that 1.65% of normal population were heterozygotes for this variant allele. These findings suggest that this substitution in exon 6 is not responsible for the type III protein S deficiency but a phenotypically neutral polymorphism. Hereby we designate this polymorphism as PS-732.