Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)

Zhou, Yang

doi:10.1007/978-1-0716-3024-2_11

Cited by 3 publications

(2 citation statements)

References 16 publications

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“…To this end, in this study, we used specific-locus amplified fragment (SLAF) sequencing (SLAF-seq) (Zhou and Pan, 2023) techniques to obtain individual DNA information from 130 XBG cattle. The published data for KZ, BS, and XBH cattle from 48 WGS analyses were downloaded from NCBI and combined with the SLAF-seq data of 129 XBG cattle for joint analysis; the proven feasibility of merging two types of data has previously confirmed the findings of an exploration of olive diversity in plants (Friel et al, 2021) and an assessment of the adaptation of Nigerian cattle in animals (Mauki et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

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

Wang,

Ma,

Gao

et al. 2024

Front. Genet.

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Introduction: Xinjiang Brown cattle are a famous dual-purpose (dairy-beef) cultivated breed in China that occupy a pivotal position within the cattle breeding industry in Xinjiang, China. However, little information is available on the genetic background of this breed. To fill this research gap, we conducted a whole-genome screen using specific-locus amplified fragment sequencing to examine the genetic structure and diversity of 130 Xinjiang Brown cattle-grazing type (XBG, traditional type) cattle.Methods: A subsequent joint analysis incorporating two ancestral breeds, specifically 19 Brown Swiss (BS) foreign and nine Kazakh (KZ) Chinese cattle, as well as 20 Xinjiang Brown cattle-housing type (XBH) cattle, was used to explore the genetic background of the Xinjiang Brown cattle.Results: The results showed that, after nearly a century of crossbreeding, XBG cattle formed a single population with a stable genetic performance. The genetic structure, genetic diversity, and selection signature analysis of the two ancestral types showed highly different results compared to that of XBH cattle. Local ancestry inference showed that the average proportions of XGB cattle within the BS and KZ cattle lineages were 37.22% and 62.78%, respectively, whereas the average proportions of XBH cattle within the BS and KZ cattle lineages were 95.14% and 4.86%, respectively. Thus, XGB cattle are more representative of all Xinjiang Brown cattle, in line with their breeding history, which involves crossbreeding. Two complementary approaches, fixation index and mean nucleotide diversity, were used to detect selection signals in the four aforementioned cattle breeds. Finally, the analysis of 26 candidate genes in Xinjiang Brown cattle revealed significant enrichment in 19 Gene Ontology terms, and seven candidate genes were enriched in three pathways related to disease resistance (CDH4, SIRPB1, and SIRPα) and the endocrine system (ADCY5, ABCC8, KCNJ11, and KCNMA1). Finally, development of the core SNPs in XBG cattle yielded 8,379 loci.Conclusion: The results of this study detail the evolutionary process of crossbreeding in Xinjiang Brown cattle and provide guidance for selecting and breeding new strains of this species.

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Section: Introductionmentioning

confidence: 99%

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

Wang,

Ma,

Gao

et al. 2024

Front. Genet.

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“…Specific-locus amplified fragment sequencing (SLAF-seq) is a simplified genome sequencing technique that uses restriction endonucleases to cut DNA and sequence partial genomes. It has several distinguishing characteristics of deep sequencing to ensure accuracy of gene typing, effectively reduce sequencing costs, and pre-designed simplified representation scheme to optimize marker efficiency [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

Analysis of genetic diversity by the SLAF-seq among the farmed Onychostoma macrolepis populations

Yang,

Han,

Wen

et al. 2024

BMC Res Notes

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Objective The objective of this study was to examine the genetic diversity within and between farmed populations of Onychostoma macrolepis, and to establish a foundation for enhancing the genetic resources of breeding groups through the introduction of new individuals and crossbreeding. A total of 49 individuals were subjected to sequencing using Specific-Locus Amplified Fragment Sequencing (SLAF-seq), one of the restriction site-associated DNA sequencing technologies. The single nucleotide polymorphisms(SNPs)were identified to conduct the analyzation of phylogeny population structure, principal component and genetic diversity. Results A total of 853,067 SNPs were identified. The results of the phylogenetic analysis revealed that each sample was genetically clustered into three distinct groups: ZhenPing (ZP), LanGao parents (LG), and their progeny population (LG-F1). Each population was observed to be clustered together. Analysis of population genetic diversity revealed that the observed heterozygosity (Ho) ranged from 0.200 to 0.230, the expected heterozygosity (He) ranged from 0.280 to 0.282, and the polymorphic information content (PIC) ranged from 0.228 to 0.230. These results indicate that the genetic diversity of the population is low and the signs of long-term interbreeding are obvious, but there are differences between the populations, and the genetic diversity of the population can be improved by hybridization in different regions.

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Development of single nucleotide polymorphism (SNP) markers and construction of DNA fingerprinting of Alcea rosea L. based on specific-locus amplified fragment sequencing (SLAF-seq) technology

Deng,

Li,

Chen

et al. 2024

Genet Resour Crop Evol

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Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)

Cited by 3 publications

References 16 publications

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

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

Analysis of genetic diversity by the SLAF-seq among the farmed Onychostoma macrolepis populations

Development of single nucleotide polymorphism (SNP) markers and construction of DNA fingerprinting of Alcea rosea L. based on specific-locus amplified fragment sequencing (SLAF-seq) technology

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