Development of SNP-Based Genomic Tools for the Canadian Bison Industry: Parentage Verification and Subspecies Composition

Yang, Tong; Miller, Michelle L.; Forgacs, David; Derr, James N.; Stothard, Paul

doi:10.3389/fgene.2020.585999

Cited by 10 publications

(8 citation statements)

References 39 publications

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“…Correct pedigree relationships are helpful for linkage map construction, core germplasm conservation, and breeding [ 10 ]. PE is a favorable parameter for evaluating kinship identification [ 37 ]. In this study, three types of PE (Q1, Q2, and Q3) for increasing combinations of the 45 markers had values of 100%, which showed that the parentage of the 117 tea cultivars could be accurately verified.…”

Section: Discussionmentioning

confidence: 99%

Development of SNP Markers for Original Analysis and Germplasm Identification in Camellia sinensis

Wang

Xun

Aktar

et al. 2022

Plants

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Tea plants are widely grown all over the world because they are an important economic crop. The purity and authenticity of tea varieties are frequent problems in the conservation and promotion of germplasm resources in recent years, which has brought considerable inconvenience and uncertainty to the selection of parental lines for breeding and the research and cultivation of superior varieties. However, the development of core SNP markers can quickly and accurately identify the germplasm, which plays an important role in germplasm identification and the genetic relationship analysis of tea plants. In this study, based on 179,970 SNP loci from the whole genome of the tea plant, all of 142 cultivars were clearly divided into three groups: Assam type (CSA), Chinese type (CSS), and transitional type. Most CSA cultivars are from Yunnan Province, which confirms that Yunnan Province is the primary center of CSA origin and domestication. Most CSS cultivars are distributed in east China; therefore, we deduced that east China (mainly Zhejiang and Fujian provinces) is most likely the area of origin and domestication of CSS. Moreover, 45 core markers were screened using strict criteria to 179,970 SNP loci, and we analyzed 117 well-Known tea cultivars in China with 45 core SNP markers. The results were as follows: (1) In total, 117 tea cultivars were distinguished by eight markers, which were selected to construct the DNA fingerprint, and the remaining markers were used as standby markers for germplasm identification. (2) Ten pairs of parent and offspring relationships were confirmed or identified, and among them, seven pairs were well-established pedigree relationships; the other three pairs were newly identified. In this study, the east of China (mainly Zhejiang and Fujian provinces) is most likely the area of origin and domestication of CSS. The 45 core SNP markers were developed, which provide a scientific basis at the molecular level to identify the superior tea germplasm, undertake genetic relationship analysis, and benefit subsequent breeding work.

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Section: Discussionmentioning

confidence: 99%

Development of SNP Markers for Original Analysis and Germplasm Identification in Camellia sinensis

Wang

Xun

Aktar

et al. 2022

Plants

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“…Following similar strategies from this study, we can evaluate multiple bison herds to assess the presence of domestic cattle genomics and determine the genetic diversity and uniqueness of these herds, which can act as candidates to establish new conservation satellite herds. Indeed, a recent study made use of our sequencing, and a similar strategy to identify additional SNOs and to create a SNP-based parentage test and subpopulation composition in the Canadian bison industry (Yang et al, 2020). Following similar criteria and additional samples to better understand the genomic relationships between bison herds will aid with the relocation of bison herds when parks or herds have reached their carrying capacity.…”

Section: Discussionmentioning

confidence: 99%

De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification

et al. 2021

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Genomic tools have improved the ability to manage bison populations and enhanced efforts to conserve this iconic species. These tools have been particularly useful for detecting introgression of cattle genome within bison herds but are limited by the need to use the cattle genome as a surrogate for mapping reads. This complicates efforts to distinguish the species of origin of chromosomal segments in individual bison at the genomic level. An assembly (Bison_UMD1.0) based on 75X genome coverage by Illumina and 454 reads was generated using the MaSuRCA assembler, generating a 2.81 Gigbases de novo reference genome from American bison. Comparison of bison and domestic cattle references identified 28 443 364 single nucleotide variants and 2 627 645 insertions/deletions distinguishing the species. Sequence alignment of an additional 12 modern bison samples and two historic bison samples to domestic cattle and bison references provides a dataset of genomic variants defining the different species and within-species variation. This first annotated draft assembly represents a resource for the management and conservation of bison, as well as a means to study the effects on the genome of interspecies hybridization. The comparisons of historical bison sequences with the new bison reference identified genomic differences between modern and pre-population bottleneck bison. The results support the application of genomics to enhance future research on disease, the establishment of satellite conservation herds and insight into bison and cattle speciation. The first genome assembly for bison and dataset provides a foundation that can be built upon as genetic technologies improve over the years.

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“…The six historical bison samples were handled and stored separately from the modern samples and DNA was extracted in a UV killing isolation station with dedicated equipment and reagents as described by Curry and Derr 39 . Most of the genomic libraries were prepared and sequenced by Delta Genomics (Edmonton, Alberta, Canada) using the methods described by Yang et al 41 . Additional genomic libraries (Mackenzie Bison Sanctuary, Vermejo Park Ranch, and Yellowstone_1925) were prepared by Texas A&M AgriLife Genomics and Bioinformatics Service (College Station, TX) and sequenced using the Illumina NovaSeq 6000 platform.…”

Section: Methodsmentioning

confidence: 99%

Genomic evaluation of hybridization in historic and modern North American Bison (Bison bison)

Stroupe

Forgacs

Harris

et al. 2022

Sci Rep

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During the late nineteenth century North American bison underwent a significant population bottleneck resulting in a reduction in population size of over 99% and a species-level near-extinction event. Factors responsible for this destruction included indiscriminate killing, loss of access to suitable habitat, and diseases. At the nadir of this population crash, very few wild plains bison survived and were restricted to Yellowstone National Park, USA and a small number of wild wood bison remained in Wood Buffalo National Park, Canada. However, most surviving bison in the late 1800’s were maintained by cattle ranchers in private herds where hybridization between bison with various breeds of domestic cattle was often encouraged. Over the last 20 years, the legacy of this introgression has been identified using mitochondrial DNA and limited nuclear microsatellite analyses. However, no genome-wide assessment has been performed, and some herds were believed to be free of introgression based on current genetic testing strategies. Herein, we report detailed analyses using whole genome sequencing from nineteen modern and six historical bison, chosen to represent the major lineages of bison, to identify and quantitate signatures of nuclear introgression in their recent (within 200 years) history. Both low and high coverage genomes provided evidence for recent introgression, including animals from Yellowstone, Wind Cave, and Elk Island National Parks which were previously thought to be free from hybridization with domestic cattle. We employed multiple approaches, including one developed for this work, to identify putative cattle haplotypes in each bison genome. These regions vary greatly in size and frequency by sample and herd, though we detected domestic cattle introgression in all bison genomes tested. Since our sampling strategy spanned across the diversity of modern bison populations, these finding are best explained by multiple historical hybridization events between these two species with significant genetic recombination over the last 200 years. Our results demonstrate that whole genome sequencing approaches are required to accurately quantitate cattle introgression in bison.

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Development of SNP-Based Genomic Tools for the Canadian Bison Industry: Parentage Verification and Subspecies Composition

Cited by 10 publications

References 39 publications

Development of SNP Markers for Original Analysis and Germplasm Identification in Camellia sinensis

Development of SNP Markers for Original Analysis and Germplasm Identification in Camellia sinensis

De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification

Genomic evaluation of hybridization in historic and modern North American Bison (Bison bison)

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