Whole-genome resequencing reveals selection signatures associated with milk production traits in African Kenana dairy zebu cattle

The study was carried out on 19 ewes of local Awassi sheep and 12ewes local Arabi sheep in the Al-kafeel sheep station Karbala, to determine the effect of breed and some non-genetic factors such as (sex of the lamb, type of birth, age and weight of ewes at birth) on daily and total milk production and lactation period and some of milk components (fat, protein and lactose). The results showed that a significant effect (P <0.05) of the breed on milk production traits where Awassi sheep recorded the highest mean (0.91 kg , 101.63 kg , 104.86 day) compared to the Arabi sheep she was means (0.77 kg , 88.15 kg , 99.15 day) respectively. As well as in proportions of milk components with mean( 5.1 , 4.90 , 5.51) % respectively compared to the Arabi sheep (4.70 . 4.20 . 4.89) ewes with male lambs also exceeded superior ewes with female lambs in daily and total milk production and the lactation period the sex of the lamb did not affect the proportions of milk components the weight of the ewes had a significant effect (P <0.05) in milk production attributes with superior weight of ewes on lower ewes and did not affect the proportions of milk ingredients except for lactose. The type of birth and the age of the ewes did not have a significant effect in all the studied traits except for the superiority (P<0.05) of young ewes on age ewes in the fat percentage of milk.

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An association analysis between PRL genotype and milk production traits in Italian Mediterranean river buffalo

Journal of Dairy Research ◽

10.1017/s0022029917000693 ◽

2017 ◽

Vol 84 (4) ◽

pp. 430-433 ◽

Cited By ~ 6

Author(s):

Jun Li ◽

Aixin Liang ◽

Zipeng Li ◽

Chao Du ◽

Guohua Hua ◽

...

Keyword(s):

Milk Production ◽

Milk Yield ◽

Milk Fat ◽

Fat Content ◽

Phenotypic Variance ◽

River Buffalo ◽

Production Traits ◽

Milk Production Traits ◽

Exon 2 ◽

Mediterranean River

This Research Communication describes the association between genetic variation within the prolactin (PRL) gene and the milk production traits of Italian Mediterranean river buffalo (Bufala mediterranea Italiana). High resolution melting (HRM) techniques were developed for genotyping 465 buffaloes. The association of genetic polymorphism with milk production traits was performed and subsequently the effects of parity and calving season were evaluated. Single nucleotide polymorphisms (SNPs) were identified at exons 2 and 5 and at introns 1 and 2. All the SNPs were in Hardy–Weinberg equilibrium, and statistical analysis showed that the polymorphism of intron1 was significantly (P < 0·05) associated with milk yield, milk protein content and peak milk yield. The average contribution of the intron1 genotype (r2intron1) to total phenotypic variance in milk production traits was 0·09, and the TT genotype showed lower values than CC and CT genotypes. A nonsynonymous SNP was identified in exon 2, which resulted in an amino acid change from arginine to cysteine. Moreover, the polymorphism of exon 2 was associated significantly with milk fat content (P < 0·05), and the buffaloes with TT genotype showed higher total fat content than the buffaloes with CT genotype. These findings provide evidence that polymorphisms of the buffalo PRL gene are associated with milk production traits and PRL can be used as a candidate gene for marker-assisted selection in Italian Mediterranean river buffalo breeding.

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Genetic diversity and population structure of Tibetan sheep breeds determined by whole genome resequencing

Tropical Animal Health and Production ◽

10.1007/s11250-021-02605-6 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Lei-Lei Li ◽

Shi-Ke Ma ◽

Wei Peng ◽

You-Gui Fang ◽

Hai-Rui Duo ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Whole Genome ◽

Genome Resequencing ◽

Sheep Breeds ◽

Tibetan Sheep ◽

Whole Genome Resequencing

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Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

Scientific Reports ◽

10.1038/s41598-021-87445-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Luciano Calderón ◽

Nuria Mauri ◽

Claudio Muñoz ◽

Pablo Carbonell-Bejerano ◽

Laura Bree ◽

...

Keyword(s):

Genetic Diversity ◽

Somatic Mutations ◽

Clonal Propagation ◽

Variant Calling ◽

Vitis Vinifera L ◽

Whole Genome ◽

Single Nucleotide Variants ◽

Genome Resequencing ◽

Diversity Pattern ◽

Whole Genome Resequencing

AbstractGrapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.

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