Estimation of variance components for carcass traits in Japanese Black cattle using 50K SNP genotype data

Genomic selection using high‐density single nucleotide polymorphism (SNP) genotype data may accelerate genetic improvements in livestock animals. In this study, we attempted to estimate the variance components of six carcass traits in fattened Japanese Black steers using SNP genotype data. Six hundred and seventy‐three steers were genotyped using an Illumina Bovine SNP50 BeadChip and phenotyped for cold carcass weight, ribeye area, rib thickness, subcutaneous fat thickness, estimated yield percent and marbling score. Additive polygenic variance and the variance attributable to a set of SNPs that had statistically significant effects on the trait were estimated via Gibbs sampling with two models: (i) a model with the chosen SNPs and the additive polygenic effects; and (ii) a model with the polygenic effects alone. The proportion of the estimated variance attributable to the SNPs became higher as the number of SNP effects that fit increased. High correlations between breeding values estimated with the model containing the polygenic effect alone and those estimated by chosen SNPs were obtained. No fraction of the total genetic variance was explained by SNPs associated with the trait at P ≥ 0.1. Our results suggest that for the carcass traits of Japanese Black cattle, a maximum of half of the total additive genetic variance may be explained by SNPs between 100 several tens to several 100s.     

Multiple marker effects of single nucleotide polymorphisms in three genes,AKIRIN2, EDG1 and RPL27A,for marbling development in Japanese Black cattle

Marbling in beef, measured by Beef Marbling Standard (BMS) number, is an economically important trait for beef cattle breeding and markets in Japan. We previously detected three single nucleotide polymorphisms (SNPs) associated with BMS number of Japanese Black in Oita prefecture: c.*188G>A in AKIRIN2, g.1471620G>T in EDG1 and g.3109537C>T in RPL27A. Here, we carried out single and multiple marker association analyses for the three SNPs in a different commercial Japanese Black population of 892 genotyped animals. The single marker analyses with the model including a single SNP showed significant associations of all SNPs with BMS number. The multiple marker analysis with the model including the main effects of the three SNPs and their interactions detected only significant main effects of g.1471620G>T and g.3109537C>T and a significant interaction between c.*188G>A and g.1471620G>T. These findings suggest the presence of inter‐allelic interactions among genes affecting the development of beef marbling. For effective marker‐assisted selection for BMS number, interactions among these markers need to be considered.     

Identification of novel genetic markers and evaluation of genetic structure in a population of Japanese crested ibis

Japanese population of the Japanese crested ibis Nipponia nippon was founded by five individuals gifted from the People's Republic of China. In order to exactly evaluate genetic structure, we first performed development of novel genetic makers using 89 microsatellite primer pairs of related species for cross‐amplification. Of these, only three primer pairs were useful for the genetic markers. Additionally, we sequenced allelic PCR products of these three markers together with 10 markers previously identified. Most markers showed typical microsatellite repeat units, but two markers were not simple microsatellites. Moreover, over half of the markers did not have the same repeat units as those of the original species. These results suggested that development of novel genetic markers in this population by cross‐amplification is not efficient, partly because of low genetic diversity. Furthermore, the cluster analysis by STRUCTURE program using 17 markers showed that the five founders were divided into two clusters. However, the genetic relationships among the founders indicated by the clustering seemed to be questionable, because the analysis relied largely on a small number of triallelic markers, in spite of the addition of the three useful markers. Therefore, more efficient methods for identifying large numbers of single nucleotide polymorphisms are desirable.     

Formation of callose from sucrose in cotton fiber microsomal membranes

Callose is formed from exogenous sucrose by cotton fiber microsomal membranes that contain both sucrose synthase and callose synthase activity. Although the coupled reaction between sucrose and callose synthases occurs predominantly to channel glucose from sucrosederived uridine diphosphate (UDP)-glucose into callose in the membranes, there is no difference in the UDP-glucose-forming/sucrose-forming activity ratios between the soluble and membrane-bound forms of sucrose synthase. The consumption of UDP-glucose from sucrose into callose probably leads to UDP-glucose formation rather than sucrose formation despite the lower affinity of sucrose synthase for sucrose than for UDP-glucose. Callose formation is markedly stimulated by the addition of either recombinant Glu¹¹ (S11E) or in vitro phosphorylated Ser¹¹ mung bean sucrose synthase but not by the wild-type nonphosphorylated Ser¹¹ enzyme. We propose that a negative charge (by phosphorylation or mutagenesis) at Ser¹¹ in sucrose synthase causes the enzyme to promote a coupled callose-forming reaction.Part of this paper was presented at the 8th International Cell Wall Meeting, Norwich, UK, September 1998     

Effects of elevation and postharvest disturbance on the composition of vegetation established after the clear-cut harvest of conifer plantations in southern Shikoku, Japan

Large areas of previously clear-cut conifer plantations have been recently abandoned in Japan. We investigated the vegetation in the clear-cut sites and examined the environmental factors affecting species composition of the vegetation. We set up 32 study sites, each composed of several study plots (5 × 5 m), ranging from 220 m to 1060 m a.s.l. Elevation and warmth index (cumulated thermal quantity) were the primary factors affecting the species composition, with clear-cut areas showing a smaller effect in the nonmetric multidimensional scaling (NMS) ordination. Two-way indicator species analysis (TWINSPAN) divided the 32 study sites into ten vegetation groups, clustering the sites by elevation or by postharvest disturbances (i.e., replanting or browsing of Sika deer). Deciduous trees and shrubs were significant in the vegetation cover at higher elevations, while they were less so in areas of high Sika deer populations. We also investigated the abundance of old-growth species, which are expected to regenerate where the clear-cut site is abandoned. Evergreen Quercus and Castanopsis saplings were abundant at low elevations (<600 m), suggesting that they will successfully regenerate. The sapling densities of Abies firma and Betula grossa were significantly large where a clear-cut site was adjacent to natural forest, which is expected to act as a seed source. This implies that degraded deciduous forests may establish after clear-cutting at intermediate and high elevations (>600 m) if the clear-cut site is distinct from seed sources. It is argued that the preservation of natural forests is critical for the regeneration of old-growth species.     

The relationship between sap flow rate and diurnal change of tangential strain on inner bark in Cryptomeria japonica saplings

The relationship between sap flow rates and diurnal fluctuation of stems was investigated in cloned 3-year-old saplings of Cryptomeria japonica D. Don grown in a phytotron with irrigation every 2 days. The improved stem heat balance method and a strain gauge were used to measure sap flow rate and diurnal fluctuation of the stem. The sap flow rate reacted to lighting conditions, increasing and decreasing immediately after lights-on and lights-off, respectively. The tangential strain on the surface of the inner bark exhibited a reaction that followed but opposed the reaction of the sap flow rate to lighting conditions. Based on the changes in sap flow rate, there seemed to be four phases in diurnal sap flow: phase A₁ began with lights-on, when the sap flow rate increased, and lasted about 2 hours. In the following phase, A₂, the sap flow rate remained almost constant at 1.3 g/min for about 10 h, and then declined for about 2 h as lights-off approached. In phase B, the early period of darkness, the sap flow declined quickly and then more slowly, for about 4 h, until the start of the second dark period, phase C, when the sap flow rate became almost constant at 0.05 g/min for about 6 h. The first derivative of each sap flow rate and the corresponding tangential strain were calculated, and the results indicated a negative correlation between the two variables in all periods. In particular, the relationship between the first derivative values exhibited a highly negative correlation in phases A₁ and B, expressed as a primary formula. Sap flow rate was found to continue for some time after lights-off, and this compensated for reduced evaporative effects, albeit at a slow rate, over 4 h. The total amount of sap flow in the dark was only about 9% of that in the light, disregarding transpiration in the dark for simplicity. Thus, the total amount of sap flow responsible for swelling of the stem was about 9% of that consumed in transpiration during the light period.