Genomic Selection for Milk Production Traits in Xinjiang Brown Cattle

Abstract

One-step genomic selection is a method for improving the reliability of the breeding value estimation. This study aimed to compare the reliability of pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP), single-trait and multitrait models, and the restricted maximum likelihood (REML) and Bayesian methods. Data were collected from the production performance records of 2207 Xinjiang Brown cattle in Xinjiang from 1983 to 2018. A cross test was designed to calculate the genetic parameters and reliability of the breeding value of 305 daily milk yield (305 dMY), milk fat yield (MFY), milk protein yield (MPY), and somatic cell score (SCS) of Xinjiang Brown cattle. The heritability of 305 dMY, MFY, MPY, and SCS estimated using the REML and Bayesian multitrait models was approximately 0.39 (0.02), 0.40 (0.03), 0.49 (0.02), and 0.07 (0.02), respectively. The heritability and estimated breeding value (EBV) and the reliability of milk production traits of these cattle calculated based on PBLUP and ssGBLUP using the multitrait model REML and Bayesian methods were higher than those of the single-trait model REML method; the ssGBLUP method was significantly better than the PBLUP method. The reliability of the estimated breeding value can be improved from 0.9% to 3.6%, and the reliability of the genomic estimated breeding value (GEBV) for the genotyped population can reach 83%. Therefore, the genetic evaluation of the multitrait model is better than that of the single-trait model. Thus, genomic selection can be applied to small population varieties such as Xinjiang Brown cattle, in improving the reliability of the genomic estimated breeding value.

Genome-wide survey reveals the genetic background of Xinjiang Brown cattle in China

“…Xinjiang Brown cattle were selectively bred during the early 20th century, in which the Kazakh (KZ) cow was the female parent and underwent three-stage hybridization with the Brown Swiss (BS) bull or the Kostroma or Ala-Tau bulls, two breeds of Brown Swiss cattle origin (Yurchenko et al, 2017). As a result, the Ministry of Agriculture of China certified the Xinjiang Brown as a novel dual-purpose (dairy-beef) cattle breed in 1983 (Zhang et al, 2022). In the following 40 years, this breed has also transitioned into the expansion phase of selection and improvement (1987)(1988)(1989)(1990)(1991)(1992)(1993)(1994)(1995)(1996)(1997)(1998)(1999)(2000)(2001)(2002)(2003)(2004)(2005)(2006), followed by a breeding phase of specialized strains (2007 to present).…”

“…In recent years, developments in genomic technology have facilitated genomic analyses that have enabled access to individual DNA information via whole-genome sequencing (WGS) (Yin et al, 2019) and genotype-by-sequencing (GBS) (Elshire et al, 2011). Research on Xinjiang Brown cattle has also entered the omics era, as evidenced by genome-wide association studies for milk production and reproductive traits (Zhou et al, 2019), genome-wide identification and analysis of long non-coding RNAs in the longest dorsal muscle tissue (Yan et al, 2021), and genomic selection for milk production traits (Zhang et al, 2022). A WGS analysis was also performed to study the genetic evolution of Xinjiang Brown cattle, which more comprehensively revealed their genetic background, genetic diversity, and adaptive mechanisms (Chen et al, 2022a); however, the samples used in this study were not genuinely representative, as all 50 samples were collected from Xinjiang Brown cattle-housing type (XBH) cattle (Figure 1D) at the Urumqi breeding farm, XBH accounts for less than 3 percent of the total number of Xinjiang Brown cattle.…”

Untitled

“…It should be noticed that can genomic selection can be implement in any dairy breed without increasing the level of investment (Obšteter et al, 2021). Reliability of genomic estimated breeding values in small dairy populations can be considerably increased by using multi-trait single step genomic BLUP (Zhang et al, 2022).…”

Incorporating the pedigree information in multi-environment trial analyses for improving common vetch

“…(2008) in a study of the social effects in the heritable variance for domestic pigs. Current studies ( Melnikova et al., 2021 ; Zhang et al., 2022 ; Kaseja et al., 2023 ) combine the classical pedigree relationships with those obtained from genetic marker data to obtain more accurate predictions of breeding values ( Aguilar et al., 2010 ).…”