Genome-wide detection of markers associated with early leaf spot and pod weight in groundnut using SNP and DArT markers

ABSTRACT

Early leaf spot (ELS) disease, caused by Cercospora arachidicola S. Hori, severely affects groundnut (Arachis hypogaea L.) production worldwide. Breeding for resistant varieties using conventional breeding is difficult because multiple genes control the resistance and heritability is moderate. Our objective was to identify marker-trait associations (MTAs) for ELS resistance in a mini-core collection of 168 accessions. The accessions were genotyped using diversity array technology (DArTseq™) and phenotyped at two locations with and without inoculation. Two types of DArTseq markers were scored; Silico DArT markers and biallelic single nucleotide polymorphism (SNP) markers. Genotype effects were significant for both ELS and pod weight (PW), with several accessions showing good levels for resistance. The heritability of ELS was moderate (0.37 to 0.64), whereas heritability for PW was low (0.10 to 0.18). The DArTseq generated 3592 biallelic SNP markers and 15,237 dominant silico markers. The distribution of the biallelic and dominant markers across the genome shows that chromosomes B04 and A04 had the highest number of markers. The MTA analysis revealed 25 significant (p < 0.001) MTAs. One MTA for ELS was found across treatments and rating dates and may be suitable for marker-assisted selection upon validation. No MTA for PW was repeatable. The germplasm and markers identified in this study can serve as useful genomic resources to initiate marker-assisted selection and trait introgression for ELS resistance in groundnut.

KEYWORDS:

• DArT-seq™
• early leaf spot
• groundnut
• marker-trait association
• pod weight
• single nucleotide polymorphism

Acknowledgments

We thank the International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Kano Station, Nigeria, for the field phenotyping. There is no grant number attached to the funding received for this research.

Disclosure statement

The authors declare that there is no conflict of interest.

Additional information

Funding

This research was supported by the Biosciences eastern and central Africa (BecA-ILRI Hub), Nairobi, Kenya and Australia through the Integrated Genotyping Service and Support (IGSS) platform for Africa.