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New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses

Tsehay, Sewalem and Ortiz Rios, Rodomiro Octavio and Johansson, Eva and Bekele, Endashaw and Tesfaye, Kassahun and Hammenhag, Cecilia and Geleta, Mulatu Dida (2020). New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses. Genes. 11 , 1373
[Research article]

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Abstract

The development and use of genomic resources are essential for understanding the population genetics of crops for their efficient conservation and enhancement. Noug (Guizotia abyssinica) is an economically important oilseed crop in Ethiopia and India. The present study sought to develop new DNA markers for this crop. Transcriptome sequencing was conducted on two genotypes and 628 transcript sequences containing 959 single nucleotide polymorphisms (SNPs) were developed. A competitive allele-specific PCR (KASP) assay was developed for the SNPs and used for genotyping of 24 accessions. A total of 554 loci were successfully genotyped across the accessions, and 202 polymorphic loci were used for population genetics analyses. Polymorphism information content (PIC) of the loci varied from 0.01 to 0.37 with a mean of 0.24, and about 49% of the loci showed significant deviation from the Hardy-Weinberg equilibrium. The mean expected heterozygosity was 0.27 suggesting moderately high genetic variation within accessions. Low but significant differentiation existed among accessions (FST = 0.045, p < 0.0001). Landrace populations from isolated areas may have useful mutations and should be conserved and used in breeding this crop. The genomic resources developed in this study were shown to be useful for population genetics research and can also be used in, e.g., association genetics.

Authors/Creators:Tsehay, Sewalem and Ortiz Rios, Rodomiro Octavio and Johansson, Eva and Bekele, Endashaw and Tesfaye, Kassahun and Hammenhag, Cecilia and Geleta, Mulatu Dida
Title:New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses
Series Name/Journal:Genes
Year of publishing :2020
Volume:11
Article number:1373
Number of Pages:23
Publisher:MDPI
ISSN:2073-4425
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Keywords:genetic diversity, genotyping, Guizotia, Hardy-Weinberg equilibrium, heterozygosity, KASP markers, noug, population structure, SNPs, transcriptome
URN:NBN:urn:nbn:se:slu:epsilon-p-109804
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-109804
Additional ID:
Type of IDID
DOI10.3390/genes11111373
Web of Science (WoS)000594012300001
ID Code:21260
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(LTJ, LTV) > Department of Plant Breeding (from 130101)
Deposited By: SLUpub Connector
Deposited On:18 Jan 2021 12:43
Metadata Last Modified:18 Jan 2021 12:51

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