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CN-122012746-A - Haplotype marker for breeding milk yield characteristics of dairy cows and application thereof

CN122012746ACN 122012746 ACN122012746 ACN 122012746ACN-122012746-A

Abstract

The invention relates to the field of molecular biology and discloses a haplotype marker for breeding milk yield characteristics of dairy cows and application thereof, wherein the haplotype marker consists of 3 SNP loci in a strong linkage disequilibrium state, the 3 SNP loci are positioned in a Block1 haplotype Block region of chromosome 10 NC_037337.1 of a dairy cow ARS-UCD1.2 genome, the 3 SNP loci are SNP 1:g.59680573A > C, SNP 2:g.59743173G > C and SNP 3:g.59743414C > T, the dominant haplotype of the haplotype marker is H2, the allele combination of the dominant haplotype marker is SNP1-A, SNP2-G, SNP-C, and the homozygous H2H2 of the dominant haplotype H2 is obviously related to the milk yield characteristics of the dairy cows. The invention solves the bottleneck of the traditional technology, remarkably improves the breeding accuracy, has stable and reliable screening and detecting technical scheme and wide application range, and improves the milk quality of groups and the industrial economic value by application.

Inventors

  • FENG XIAOFANG
  • GUO PENGHUI
  • Zheng Juanshan
  • PEI SHENGWEI
  • ZHANG YONG

Assignees

  • 西北民族大学

Dates

Publication Date
20260512
Application Date
20260403

Claims (10)

  1. 1. A haplotype marker for breeding milk yield characteristics of dairy cows, which is characterized by comprising 3 SNP loci in a strong linkage disequilibrium state, wherein the 3 SNP loci are positioned in a Block1 haplotype Block region of a 10 # chromosome NC_037337.1 of a dairy cow ARS-UCD1.2 genome; the 3 SNP loci are: SNP1:g.59680573 A>C, SNP2:g.59743173 G>C, SNP3:g.59743414 C>T; the dominant haplotype of the haplotype mark is H2, the allele combination is SNP1-A, SNP2-G, SNP-C, and the homozygote H2H2 of the dominant haplotype H2 is obviously related to the high milk fat percentage of milk cows.
  2. 2. The haplotype marker of claim 1, wherein the dairy cow milk high milk fat rate trait is a dairy cow milk fat rate trait at a lactation period of 305 days.
  3. 3. The haplotype marker of claim 1 wherein the cow is a Holstein cow.
  4. 4. A specific primer probe set for detecting the haplotype marker according to claim 1, which comprises an upstream primer, a downstream primer and a specific probe aiming at SNP1, SNP2 and SNP3 loci, and is characterized in that: (1) Aiming at SNP1 locus, the upstream primer sequence is shown as SEQ ID NO.1, the downstream primer sequence is shown as SEQ ID NO.2, and the probe sequence is shown as SEQ ID NO. 3; (2) For SNP2 locus, the upstream primer sequence is shown as SEQ ID NO.4, the downstream primer sequence is shown as SEQ ID NO.5, and the probe sequence is shown as SEQ ID NO. 6; (3) For SNP3 locus, the upstream primer sequence is shown as SEQ ID NO.7, the downstream primer sequence is shown as SEQ ID NO.8, and the probe sequence is shown as SEQ ID NO. 9.
  5. 5. The set of specific primer probes of claim 4, wherein the probes are SBE probes.
  6. 6. A kit for detecting the haplotype marker of claim 1, comprising the specific primer probe set of claim 4, and optionally comprising PCR reaction buffer, DNA polymerase, dNTP mix, DNA extraction reagents, and genotyping reagents.
  7. 7. The kit according to claim 6, further comprising a positive control and a negative control, wherein the positive control is a dairy cow genomic DNA standard carrying an H2H2 homozygous haplotype combination, and the negative control is nuclease-free ultrapure water.
  8. 8. Use of a haplotype marker according to any one of claims 1-3, or a specific primer probe set according to any one of claims 4-5, or a kit according to any one of claims 6-7, for milk cow milk yield trait molecular marker assisted selection, genome selection, or milk cow milk yield trait genotype identification.
  9. 9. The use according to claim 8, characterized by the steps of: (1) Collecting biological samples of cows to be tested, and extracting genome DNA; (2) Genotyping the 3 SNP sites of claim 1 in the genomic DNA, constructing haplotypes and determining a haplotype combination of an individual to be tested; (3) And screening individuals carrying the H2H2 homozygous haplotype combination as seed reserving individuals of a dairy cow breeding group, and breeding a dairy cow strain with high milk fat rate.
  10. 10. The use according to claim 9, wherein the genotyping method comprises any one of Sanger sequencing, time-of-flight mass spectrometry, taqMan probe, gene chip, high throughput sequencing.

Description

Haplotype marker for breeding milk yield characteristics of dairy cows and application thereof Technical Field The invention relates to the field of molecular biology, in particular to a haplotype marker for breeding milk fat rate characteristics of dairy cows and application thereof. Background Milk is a core animal product with both nutritive value and economic value, and occupies a core strategic position in the high-quality development of animal husbandry in China. In recent years, as consumer consumption upgrades, the market demand for high-end dairy products continues to rise, and milk quality becomes a core focus of industry competition and consumer attention. Milk fat is a core index for evaluating milk quality, not only determines the flavor, the nutritional value and the processing characteristics of milk, but also is a key basis for purchasing and pricing fresh milk, and the content of the milk fat directly determines the core competitiveness of a milk industry chain. Holstein cows are the most widely cultivated cow varieties with the highest milk yield, and are the dominant varieties of cow cultivation in China, but the milk fat rate is low as a whole, the average industrial level is only about 3.5%, the lack of fine variety with high milk fat rate becomes a core bottleneck for restricting the quality improvement and synergy of milk industry in China and improving the international competitiveness, and the genetic regulation and fine variety breeding of milk fat traits become research hotspots and hardness attack points in the field of cow cultivation in China. The milk production character of the dairy cow belongs to complex quantitative characters controlled by micro-effect polygenes, the genetic factors are fundamental factors for determining core economic characters such as milk fat, and the excellent genetic characters can be stably transferred in generations. The traditional dairy cow breeding system takes variety registration, DHI production performance measurement and descendant measurement as cores, plays an important role in improving the milk yield of dairy cows, but has the inherent limitations of long generation interval, slow genetic progress, great influence on the selection accuracy by environment and the like, and cannot meet the breeding requirement of the dairy industry in China on the rapid improvement of the milk fat percentage property. 20. In the 80 s of century, along with the deep fusion of molecular genetics and quantitative genetics, molecular breeding technology rapidly develops, and milk cow breeding is pushed to span from traditional phenotype selection to genotype precise selection. Wherein, marker Assisted Selection (MAS) breeding is one of core technologies for genetic improvement of economic traits of cows by virtue of the advantages of directly selecting target trait genotypes, greatly shortening generation intervals and improving selection accuracy. The core premise of MAS breeding is to mine and obtain molecular genetic markers which are obviously related to target traits, have stable genetic effects and can explain higher phenotypic variation. In recent years, the whole genome selection (GS, genomic selection) technology is widely applied to cow breeding, and the essence of the technology is the auxiliary selection of high-density whole genome markers, so that early and accurate seed selection of young cows can be realized, and the breeding efficiency is further improved. However, the existing researches show that the estimation accuracy of the genome breeding value of GS is highly dependent on the integration of functional genes and major genetic markers obviously related to target traits, and the selection accuracy of low-genetic traits such as milk fat rate is limited only by virtue of randomly distributed whole genome SNP markers. The Single Nucleotide Polymorphism (SNP) is the most widely used molecular marker at present, and a haplotype marker formed by a plurality of SNP loci which are closely linked and in a strong linkage disequilibrium state can reflect the genetic effect of a target gene more stably than a single SNP locus, has higher association degree with complex quantitative characters, can explain phenotype variation with higher proportion, and is a more ideal genetic marker for cow molecular breeding. At present, aiming at the milk fat percentage character of Holstein cows in China, haplotype marks with obvious genetic effects are still very deficient through large-population scale verification, and the efficiency and the accuracy of molecular breeding of the milk fat percentage character are severely restricted. Therefore, the dominant haplotype marker obviously related to the milk fat percentage character of the Holstein cows is mined and verified, and an accurate and efficient molecular tool is provided for breeding the high milk fat percentage strain of the cows, so that the dominant haplotype marker is a key technical problem to be solv