基于多性状模型内蒙古绒山羊早期生长性状基因组预测准确性研究
收稿日期: 2024-01-31
修回日期: 2024-04-25
网络出版日期: 2024-05-06
基金资助
国家重点研发计划项目(2022YFE0113300);国家重点研发计划项目(2022YFD1300201);国家重点研发计划项目(2022YFD1300204);内蒙古自治区科技攻关项目(2021GG0086);内蒙古自治区高等学校“青年科技英才支持计划”(NJYT22038);财政部和农业农村部:国家绒毛用羊产业技术体系项目(CARS-39);内蒙古农业大学高水平成果培育专项(QT202201);内蒙古自治区高等学校创新团队发展计划项目(NMGIRT2322);内蒙古自治区直属高校基本科研业务费项目(BR220112)
Comparison of genomic prediction methods for early growth traits of Inner Mongolia cashmere goats based on multi trait models
Received date: 2024-01-31
Revised date: 2024-04-25
Online published: 2024-05-06
Supported by
National Key Research and Development Program(2022YFE0113300);National Key Research and Development Program(2022YFD1300201);National Key Research and Development Program(2022YFD1300204);Inner Mongolia Autonomous Region Science and Technology Research Project(2021GG0086);Inner Mongolia Autonomous Region Higher Education Youth Science and Technology Talent Support Program(NJYT22038);Ministry of Finance and the Ministry of Agriculture and Rural Affairs, the National Technical System for Woolen Sheep Industry(CARS-39);High Level Achievement Cultivation Project of Inner Mongolia Agricultural University(QT202201);Inner Mongolia Autonomous Region Higher Education Innovation Team Development Program(NMGIRT2322);Basic Research Expenses of Universities Directly of Inner Mongolia Autonomous Region(BR220112)
内蒙古绒山羊是经过长期自然选择和人工选育后形成的优良家畜品种,是目前世界一流的绒肉兼用山羊。多性状动物模型被认为可以显著提高畜禽遗传评估的准确性,实现性状间的间接选择。本文基于内蒙古绒山羊个体的系谱、基因型、环境以及早期生长性状的表型记录,建立多性状动物模型,利用ABLUP、GBLUP、ssGBLUP三种方法进行早期生长性状(初生重、断乳重、断乳前平均日增重、周岁重)遗传参数及基因组育种值的估计,进一步利用五倍交叉验证方法评价基因组育种值估计准确性和可靠性。结果显示,3种方法估计的初生重遗传力为0.13~0.15,断乳重遗传力为0.13~0.20,日增重遗传力为0.11~0.14,周岁重遗传力为0.09~0.14,均属于中等偏低遗传力;断乳重和日增重、日增重和周岁重之间存在强的正遗传相关,相关系数分别为0.77~0.79和0.56~0.67,表型相关发现同样的规律;ABLUP、GBLUP和ssGBLUP法估计的初生重育种值准确性分别为0.5047、0.6694、0.7156,断乳重分别为0.6207、0.6456、0.7254;日增重分别为0.6110、0.6855、0.7357,周岁重分别为0.6209、0.7155、0.7756。综上所述,内蒙古绒山羊早期生长性状属于中等偏低遗传力,对其进行遗传选育改良速度相对较慢;通过对断乳重的选择可以实现其他生长性状的遗传改良;ssGBLUP方法估计内蒙古绒山羊早期生长性状基因组育种值的准确性和可靠性均最高,且显著高于ABLUP法,说明该方法是内蒙古绒山羊早期性状基因组选育的最佳方法。
关键词: 内蒙古绒山羊; 早期生长性状; 多性状动物模型; 基因组育种值估计准确性
高林豫, 许琦, 何钰霄, 习海娇, 刘一帆, 张涛, 李金泉, 张燕军, 王瑞军, 吕琦, 梅步俊, 苏蕊, 王志英 . 基于多性状模型内蒙古绒山羊早期生长性状基因组预测准确性研究[J]. 遗传, 2024 , 46(5) : 421 -430 . DOI: 10.16288/j.yczz.24-036
Inner Mongolia cashmere goat is an excellent livestock breed formed through long-term natural selection and artificial breeding, and is currently a world-class dual-purpose breed producing cashmere and meat. Multi trait animal model is considered to significantly improve the accuracy of genetic evaluation in livestock and poultry, enabling indirect selection between traits. In this study, the pedigree, genotype, environment, and phenotypic records of early growth traits of Inner Mongolia cashmere goats were used to build multi trait animal model., Then three methods including ABLUP, GBLUP, and ssGBLUP wereused to estimate the genetic parameters and genomic breeding values of early growth traits (birth weight, weaning weight, average daily weight gain before weaning, and yearling weight). The accuracy and reliability of genomic estimated breeding value are further evaluated using the five fold cross validation method. The results showed that the heritability of birth weight estimated by three methods was 0.13-0.15, the heritability of weaning weight was 0.13-0.20, heritability of daily weight gain before weaning was 0.11-0.14, and the heritability of yearling weight was 0.09-0.14, all of which belonged to moderate to low heritability. There is a strong positive genetic correlation between weaning weight and daily weight gain before weaning, daily weight gain before weaning and yearling weight, with correlation coefficients of 0.77-0.79 and 0.56-0.67, respectively. The same pattern was found in phenotype correlation among traits. The accuracy of the estimated breeding values by ABLUP, GBLUP, and ssGBLUP methods for birth weight is 0.5047, 0.6694, and 0.7156, respectively; the weaning weight is 0.6207, 0.6456, and 0.7254, respectively; the daily weight gain before weaning was 0.6110, 0.6855, and 0.7357 respectively; and the yearling weight was 0.6209, 0.7155, and 0.7756, respectively. In summary, the early growth traits of Inner Mongolia cashmere goats belong to moderate to low heritability, and the speed of genetic improvement is relatively slow. The genetic improvement of other growth traits can be achieved through the selection of weaning weight. The ssGBLUP method has the highest accuracy and reliability in estimating genomic breeding value of early growth traits in Inner Mongolia cashmere goats, and is significantly higher than that from ABLUP method, indicating that it is the best method for genomic breeding of early growth weight in Inner Mongolia cashmere goats.
| [1] | Su R, Gong G, Zhang LT, Yan XC, Wang FH, Zhang L, Qiao X, Li XK, Li JQ. Screening the key genes of hair follicle growth cycle in Inner Mongolian cashmere goat based on RNA sequencing. Arch Anim Breed, 2020, 63(1): 155-164. |
| [2] | Meuwissen TH, Hayes BJ, Goddard ME. Prediction of total genetic value using genome-wide dense marker maps. Genetics, 2001, 157(4): 1819-1829. |
| [3] | Sandhu KS, Mihalyov PD, Lewien MJ, Pumphrey MO, Carter AH. Combining genomic and phenomic information for predicting grain protein content and grain yield in spring wheat. Front Plant Sci, 2021, 12: 613300. |
| [4] | Villar-Hernández BJ, Pérez-Elizalde S, Martini JWR, Toledo F, Perez-Rodriguez P, Krzuse M, García-Calvillo ID, Covarrubias-Pazaran G, Crossa J. Corrigendum to: application of multi-trait bayesian decision theory for parental genomic selection. G3 (Bethesda), 2021, 11(3): jkab034. |
| [5] | Henderson CR. Best linear unbiased estimation and prediction under a selection model. Biometrics, 1975, 31(2): 423-447. |
| [6] | Nilforooshan MA, Jakobsen JH, Fikse WF, Berglund B, Jorjani H. Application of a multiple-trait, multiple-country genetic evaluation model for female fertility traits. J Dairy Sci, 2010, 93(12): 5977-5986. |
| [7] | Galluzzo F, Visentin G, van Kaam JBCHM, Finocchiaro R, Biffani S, Costa A, Marusi M, Cassandro M. Genetic evaluation of gestation length in Italian Holstein breed. J Anim Breed Genet, 2024, 141(2): 113-123. |
| [8] | Adekale D, Alkhoder H, Liu ZT, Segelke D, Tetens J. Single-step SNPBLUP evaluation in six German beef cattle breeds. J Anim Breed Genet, 2023, 140(5): 496-507. |
| [9] | Lee SH, Lee SH, Park HB, Kim JM. Estimation of genetic parameters for pork belly traits. Anim Biosci, 2023, 36(8): 1156-1166. |
| [10] | Zhang X, Tsuruta S, Andonov S, Lourenco DAL, Sapp RL, Wang C, Misztal I. Relationships among mortality, performance, and disorder traits in broiler chickens: a genetic and genomic approach. Poult Sci, 2018, 97(5): 1511-1518. |
| [11] | Butler DG, Cullis BR, Gilmour AR, Gogel BG, Thompson R.ASReml-R Reference Manual Version 4. VSN International Ltd, Hemel Hempstead, HP1 1ES, UK. 2017. |
| [12] | Christensen OF, Madsen P, Nielsen B, Ostersen T, Su G. Single-step methods for genomic evaluation in pigs. Animal, 2012, 6(10): 1565-1571. |
| [13] | Kong J, Luan S, Tan J, Sui J, Luo K, Li XP, Dai P, Meng XH, Lu X, Chen BL, Cao JW, Cao BX. Progress of study on penaeid shrimp selective breeding. J Ocean Univ China(Nat Sci Ed), 2020, 50(9): 81-97. |
| 孔杰, 栾生, 谭建, 隋娟, 罗坤, 李旭鹏, 代平, 孟宪红, 卢霞, 陈宝龙, 曹家旺, 曹宝祥. 对虾选择育种研究进展. 中国海洋大学学报(自然科学版), 2020, 50 (9): 81-97. | |
| [14] | Aguilar I, Misztal I, Tsuruta S, Wiggans GR, Lawlor TJ. Multiple trait genomic evaluation of conception rate in Holsteins. J Dairy Sci, 2011, 94(5): 2621-2624. |
| [15] | Tsuruta S, Misztal I, Aguilar I, Lawlor TJ. Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins. J Dairy Sci, 2011, 94(8): 4198-4204. |
| [16] | Guo G, Zhao FP, Wang YC, Zhang Y, Du LX, Su GS. Comparison of single-trait and multiple-trait genomic prediction models. BMC Genet, 2014, 15: 30. |
| [17] | Roy R, Mandal A, Notter DR. Estimates of (co)variance components due to direct and maternal effects for body weights in Jamunapari goats. Animal, 2008, 2(3): 354-359. |
| [18] | Magotra A, Bangar YC, Chauhan A, Malik BS, Malik ZS. Influence of maternal and additive genetic effects on offspring growth traits in Beetal goat. Reprod Domest Anim, 2021, 56(7): 983-991. |
| [19] | Di J, Zhang Y, Tian KC, Lazate, Liu JF, Xu XM, Zhang YJ, Zhang TH. Estimation of (co)variance components and genetic parameters for growth and wool traits of Chinese superfine merino sheep with the use of a multi-trait animal model. Livest Sci, 2011, 138(1-3): 278-288. |
| [20] | Gowane GR, Chopra A, Prakash V, Arora AL. Estimates of (co)variance components and genetic parameters for growth traits in Sirohi goat. Trop Anim Health Prod, 2011, 43(1): 189-198. |
| [21] | Barazandeh A, Moghbeli SM, Vatankhah M, Mohammadabadi M. Estimating non-genetic and genetic parameters of pre-weaning growth traits in Raini cashmere goat. Trop Anim Health Prod, 2012, 44(4): 811-817. |
| [22] | Tesema Z, Alemayehu K, Getachew T, Kebede D, Deribe B, Taye M, Tilahun M, Lakew M, Kefale A, Belayneh N, Zegeye A, Yizengaw L. Estimation of genetic parameters for growth traits and Kleiber ratios in Boer × Central Highland goat. Trop Anim Health Prod, 2020, 52(6): 3195-3205. |
| [23] | 张沅. 家畜育种学. 北京: 中国农业出版社, 2001. |
| [24] | Bangar YC, Magotra A, Yadav AS. Estimates of covariance components and genetic parameters for growth, average daily gain and Kleiber ratio in Harnali sheep. Trop Anim Health Prod, 2020, 52(5): 2291-2296. |
| [25] | Wang RJ, Liu Y, Shi Y, Qi YP, Li YB, Wang ZY, Zhang YJ, Zhao YH, Su R, Li JQ. Study of genetic parameters for pre-weaning growth traits in inner Mongolia white Arbas cashmere goats. Front Vet Sci, 2023, 9: 1026528. |
| [26] | 王大广, 赵志辉, 赵玉民, 鲍志鸿. 萨福克羊表型测定值遗传参数的估计. 中国草食动物, 2003, (S1): 67-68. |
| [27] | Baloche G, Legarra A, Sallé G, Larroque H, Astruc J-M, Robert-Granié C, Barillet F. Assessment of accuracy of genomic prediction for French Lacaune dairy sheep. J Dairy Sci, 2014, 97(2): 1107-1116. |
| [28] | Negro A, Cesarani A, Cortellari M, Bionda A, Fresi P, Macciotta NPP, Grande S, Biffani S, Crepaldi P. A comparison of genetic and genomic breeding values in Saanen and Alpine goats. Animal, 2024, 18(4): 101118. |
| [29] | Wang FH.Design of goat SNP chip and genome-wide association analysis and genome selection of important economic traits in Inner Mongolia cashmere goats[Dissertation]. Inner Mongolia Agricultural University, 2021. |
| 王凤红.山羊SNP芯片设计与内蒙古绒山羊重要经济性状全基因组关联分析及基因组选择研究[学位论文]. 内蒙古农业大学, 2021. |
/
| 〈 |
|
〉 |