Yoshitaka Nagamine

Estimation of the Time of Divergence between Japanese Mishima Island Cattle and Other Cattle Populations Using Microsatellite DNA Markers

We applied the theory of random genetic drift to determine the divergence history of a closed cattle population over the relatively short timescale of several hundred years. The divergence history of the closed population of Mishima Island cattle, a national natural treasure of Japan, was examined, and the results were compared with historical documents. Inbreeding depression in the isolated population was investigated for body size and fertility. Twenty-one DNA microsatellite markers in Mishima Island cattle and 3 major breeds from the mainland were genotyped. For the mainland breeds, all 21 or 20 markers were segregating. However, nearly half the number of loci (9 of 21) was fixed in the Island cattle. The average number of alleles per locus of Island cattle was markedly lower than that in the mainland breeds. These results support the theory that Island cattle have been isolated for a considerable period of time. The number of generations of isolation was estimated as 14.1-22.6, and the year of divergence was calculated as 1778-1846. In view of these findings, we propose that Island cattle diverged from the mainland population at around 1800 and were isolated for about 200 years. These estimates are in agreement with historical documents showing that divergence occurred between 1672 and 1880. The total inbreeding coefficient of the present population was predicted to be in the range of 0.51-0.60. However, historical reports dated over 100 years do not support changes in fertility, so that there is no evidence for inbreeding depression.

Relationships between conception rate in Holstein heifers and cows and milk yield at various stages of lactation

We investigated the relationships between conception rates (CRs) at first service in Japanese Holstein heifers (i.e. animals that had not yet had their first calf) and cows and their test-day (TD) milk yields. Data included records of artificial insemination (AI) for heifers and cows that had calved for the first time between 2000 and 2008 and their TD milk yields at 6 through 305 days in milk (DIM) from first through third lactations. CR was defined as a binary trait for which first AI was a failure or success. A threshold-linear animal model was applied to estimate genetic correlations between CRs of heifers or cows and TD milk yield at various lactation stages. Two-trait genetic analyses were performed for every combination of CR and TD milk yield by using the Bayesian method with Gibbs sampling. The posterior means of the heritabilities of CR were 0.031 for heifers, 0.034 for first-lactation cows and 0.028 for second-lactation cows. Heritabilities for TD milk yield increased from 0.324 to 0.433 with increasing DIM but decreased slightly after 210 DIM during first lactation. These heritabilities from the second and third lactations were higher during late stages of lactation than during early stages. Posterior means of the genetic correlations between heifer CR and all TD yields were positive (range, 0.082 to 0.287), but those between CR of cows and milk yields during first or second lactation were negative (range, -0.121 to -0.250). Therefore, during every stage of lactation, selection in the direction of increasing milk yield may reduce CR in cows. The genetic relationships between CR and lactation curve shape were quite weak, because the genetic correlations between CR and TD milk yield were constant during the lactation period.

Genetic correlations between production and disease traits during first lactation in Holstein cows

The aim of this study was to estimate genetic correlations between milk yield, somatic cell score (SCS), mastitis, and claw and leg disorders (CLDs) during first lactation in Holstein cows by using a threshold-linear random regression test-day model. We used daily records of milk, fat and protein yields; somatic cell count (SCC); and mastitis and CLD incidences from 46 771 first-lactation Holstein cows in Hokkaido, Japan, that calved between 2000 and 2009. A threshold animal model for binary records (mastitis and CLDs) and linear animal model for yield traits were applied in our multiple trait analysis. For both liabilities and yield traits, additive genetic effects were used as random regression on cubic Legendre polynomials of days on milk. The highest positive genetic correlations between yields and disease incidences (0.36 for milk and mastitis, 0.56 for fat and mastitis, 0.24 for protein and mastitis, 0.32 for milk and CLD, 0.44 for fat and CLD and 0.31 for protein and CLD) were estimated at about the time of peak milk yield (36 to 65 days in milk). Selection focused on early lactation yield may therefore increase the risk of mastitis and CLDs. The positive genetic correlations of SCS with mastitis or CLD incidence imply that selection to reduce SCS in the early stages of lactation would decrease the incidence of both mastitis and CLD.

Lactation Persistency as a Component Trait of the Selection Index and Increase in Reliability by Using Single Nucleotide Polymorphism in Net Merit Defined as the First Five Lactation Milk Yields and Herd Life

We first sought to clarify the effects of discounted rate, survival rate, and lactation persistency as a component trait of the selection index on net merit, defined as the first five lactation milks and herd life (HL) weighted by 1 and 0.389 (currently used in Japan), respectively, in units of genetic standard deviation. Survival rate increased the relative economic importance of later lactation traits and the first five lactation milk yields during the first 120 months from the start of the breeding scheme. In contrast, reliabilities of the estimated breeding value (EBV) in later lactation traits are lower than those of earlier lactation traits. We then sought to clarify the effects of applying single nucleotide polymorphism (SNP) on net merit to improve the reliability of EBV of later lactation traits to maximize their increased economic importance due to increase in survival rate. Net merit, selection accuracy, and HL increased by adding lactation persistency to the selection index whose component traits were only milk yields. Lactation persistency of the second and (especially) third parities contributed to increasing HL while maintaining the first five lactation milk yields compared with the selection index whose only component traits were milk yields. A selection index comprising the first three lactation milk yields and persistency accounted for 99.4% of net merit derived from a selection index whose components were identical to those for net merit. We consider that the selection index comprising the first three lactation milk yields and persistency is a practical method for increasing lifetime milk yield in the absence of data regarding HL. Applying SNP to the second- and third-lactation traits and HL increased net merit and HL by maximizing the increased economic importance of later lactation traits, reducing the effect of first-lactation milk yield on HL (genetic correlation (rG) = −0.006), and by augmenting the effects of the second- and third-lactation milk yields on HL (rG = 0.118 and 0.257, respectively).

Economic effects of using sexed semen in Japanese dairy herds.

Dairy farm agricultural income should increase when sexed semen is used instead of unsexed semen. This study simulated three scenarios: using unsexed semen (N), using X sperm of Holstein and unsexed semen of Japanese Black (H), and using X sperm of Holstein and Y sperm of Japanese Black (HJ). Two management scenarios were considered: conventional management (CONV); and the use of Japanese Black semen with surplus cows to produce F(1) s where sufficient replacement female Holstein calves were obtained for maintenance (MAINT). In CONV, the agricultural incomes of H and HJ were 610,000-2,400,000 yen higher than that of N. The agricultural income increased when the difference in the prices between Holstein males and average F(1) male/female calves was 34,000-50,000 yen, that between Holstein male and female calves was 80,000-110,000 yen, and that between F(1) male and female calves was 50,000-90,000 yen. Therefore, the agricultural income can be increased by using sexed semen to select calves of a more valued breed and sex.

Detection of multiple quantitative trait loci and their pleiotropic effects in outbred pig populations

BackgroundSimultaneous detection of multiple QTLs (quantitative trait loci) may allow more accurate estimation of genetic effects. We have analyzed outbred commercial pig populations with different single and multiple models to clarify their genetic properties and in addition, we have investigated pleiotropy among growth and obesity traits based on allelic correlation within a gamete.MethodsThree closed populations, (A) 427 individuals from a Yorkshire and Large White synthetic breed, (B) 547 Large White individuals and (C) 531 Large White individuals, were analyzed using a variance component method with one-QTL and two-QTL models. Six markers on chromosome 4 and five to seven markers on chromosome 7 were used.ResultsPopulation A displayed a high test statistic for the fat trait when applying the two-QTL model with two positions on two chromosomes. The estimated heritabilities for polygenic effects and for the first and second QTL were 19%, 17% and 21%, respectively. The high correlation of the estimated allelic effect on the same gamete and QTL test statistics suggested that the two separate QTL which were detected on different chromosomes both have pleiotropic effects on the two fat traits. Analysis of population B using the one-QTL model for three fat traits found a similar peak position on chromosome 7. Allelic effects of three fat traits from the same gamete were highly correlated suggesting the presence of a pleiotropic QTL. In population C, three growth traits also displayed similar peak positions on chromosome 7 and allelic effects from the same gamete were correlated.ConclusionDetection of the second QTL in a model reduced the polygenic heritability and should improve accuracy of estimated heritabilities for both QTLs.

Transformation of QTL genotypic effects to allelic effects

The genotypic and allelic effect models are equivalent in terms of QTL detection in a simple additive model, but the QTL allelic model has the advantage of providing direct information for marker-assisted selection. However, the allelic matrix is four times as large as the genotypic IBD matrix, causing computational problems, especially in genome scans examining multiple positions. Transformation from genotypic to allelic effects, after estimating the genotypic effects with a smaller IBD matrix, can solve this problem. Although the validity of transformation from genotypic to allelic effects has been disputed, this work proves that transformation can successfully yield unique allelic effects when genotypic and allelic IBD matrixes exist.

Effects of heat stress on production, somatic cell score and conception rate in Holsteins

We examined the effects of heat stress (HS) on production traits, somatic cell score (SCS) and conception rate at first insemination (CR) in Holsteins in Japan. We used a total of 228 242 records of milk, fat and protein yields, and SCS for the first three lactations, as well as of CR in heifers and in first- and second-lactation cows that had calved for the first time between 2000 and 2012. Records from 47 prefectural weather stations throughout Japan were used to calculate the temperature-humidity index (THI); areas were categorized into three regional groups: no HS (THI < 72), mild HS (72 ≤ THI < 79), and moderate HS (THI ≥ 79). Trait records from the three HS-region groups were treated as three different traits and trivariate animal models were used. The genetic correlations between milk yields from different HS groups were very high (0.91 to 0.99). Summer calving caused the greatest increase in SCS, and in the first and second lactations this increase became greater as THI increased. In cows, CR was affected by the interaction between HS group and insemination month: with summer and early autumn insemination, there was a reduction in CR, and it was much larger in the mild- and moderate-HS groups than in the no-HS group.

Genetic Improvement on Growth Rate and Carcass Traits of Japanese Shorthorn Cattle

日本短角種の発育速度が遺伝的に改良されていることを明らかにし,今後最も重要な課題である精肉歩留り向上のために現場後代検定を行なった.1974～1985年に直接検定にかけられた雄牛のうち13頭の種雄牛の息牛183頭の成績を用いて一日平均増体量(DG)の表型価の推移,および遺伝的趨勢をみた.種雄牛の育種価はBLUP法により推定した,種雄牛の育種価の出生年次に対する回帰係数は+10.6g/年(P〈0.05)であり,息牛におけるDGの表型価の検定年次に対する回帰係数は+30.1g/年(P〈0.01)であった.1985年9月から1986年1月に出荷された1,009頭の枝肉について5～6肋骨間断面の3ヵ所の皮下脂肪厚,ロース芯面積の測定および脂肪交雑の判定を行ない,現場後代検定を実施した,皮下脂肪厚1,2,3の和および各皮下脂肪厚の平均値は63.8,25.7,21.9,16.3mm,またロース芯面積と脂肪交雑評点の平均値は40.2cm2,0.33であった.精肉量による種雄牛の順位づけを行なうため,17頭のデータを用い5～6肋骨間断面の測定値から精肉量を推定する次の重回帰式を作製した.精肉量推定値(kg)=0.492×枝肉重量(kg)-0.280×皮下脂肪厚3ヵ所の和(mm)+0.488×ロース芯面積(cm2)+33.31(R=0.95)平均枝肉重量の概数340kgと一次回帰式により340kg時の値に補正した各個体の測定値を代入して精肉量推定値を求めた.その結果,現場後代検定における精肉量推定値の平均は202,6kg,枝肉重量340kgに対する精肉歩留りの平均は59.6%であった.1,009頭の枝肉のうち26頭の種雄牛の息牛237頭のデータを用い,BLUP法により各形質のExpected Progeny Difference (EPD)を推定した.EPDは皮下脂肪厚3ヵ所の和では-6,0～+12.1mm,ロース芯面積では-3.0～＋2.9cm2,脂肪交雑評点では-0.10～+0.21の範囲であった.前述の精肉量推定式を用いて枝肉重量340kg時の種雄牛別の精肉量を求めたところ,197.9～203.9kgの推定値が得られた.

Antagonistic genetic correlations for milking traits within the genome of dairy cattle

Genome-wide association studies can be applied to identify useful SNPs associated with complex traits. Furthermore, regional genomic mapping can be used to estimate regional variance and clarify the genomic relationships within and outside regions but has not previously been applied to milk traits in cattle. We applied both single SNP analysis and regional genomic mapping to investigate SNPs or regions associated with milk yield traits in dairy cattle. The de-regressed breeding values of three traits, total yield (kg) of milk (MLK), fat (FAT), and protein (PRT) in 305 days, from 2,590 Holstein sires in Japan were analyzed. All sires were genotyped with 40,646 single-nucleotide polymorphism (SNP) markers. A genome-wide significant region (P < 0.01) common to all three traits was identified by regional genomic mapping on chromosome (BTA) 14. In contrast, single SNP analysis identified significant SNPs only for MLK and FAT (P < 0.01), but not PRT in the same region. Regional genomic mapping revealed an additional significant region (P < 0.01) for FAT on BTA5 that was not identified by single SNP analysis. The additive whole-genomic effects estimated in the regional genomic mapping analysis for the three traits were positively correlated with one another (0.830–0.924). However, the regional genomic effects obtained by using a window size of 20 SNPs for FAT on BTA14 were negatively correlated (P < 0.01) with the regional genomic effect for MLK (–0.940) and PRT (–0.878). The BTA14 regional effect for FAT also showed significant negative correlations (P < 0.01) with the whole genomic effects for MLK (–0.153), FAT (–0.172), and PRT (–0.181). These negative genomic correlations between loci are consistent with the negative linkage disequilibrium expected for traits under directional selection. Such antagonistic correlations may hamper the fixation of the FAT increasing alleles on BTA14. In summary, regional genomic mapping found more regions associated with milk production traits than did single SNP analysis. In addition, the existence of non-zero covariances between regional and whole genomic effects may influence the detection of regional effects, and antagonistic correlations could hamper the fixation of major genes under intensive selection.