Development of SSR markers and association studies of markers with phenology and yield-related traits in grass pea (Lathyrus sativus)
Khela Ram Soren
A D , Aravind Kumar Konda A , Priyanka Gangwar B , Vijay A. Tiwari C , P. S. Shanmugavadivel A , Ashok Kumar Parihar A D , Girish Prasad Dixit A and Narendra Pratap Singh A
+ Author Affiliations
- Author Affiliations
A ICAR-Indian Institute of Pulses Research, Kanpur, UP 208024, India.
B Amity Institute of Biotechnology, Amity University, Gomti Nagar Extension, Lucknow, UP 226028, India.
C Department of Biotechnology, Chatrapati Shahu Ji Maharajah University, Kanpur, UP 208024, India.
D Corresponding authors. Email: sorenars@gmail.com; ashoka.parihar@gmail.com
Crop and Pasture Science 71(8) 768-775 https://doi.org/10.1071/CP19557
Submitted: 31 December 2019 Accepted: 4 July 2020 Published: 31 July 2020
Abstract
Grass pea (Lathyrus sativus L.) is an important food crop cultivated in dryland agricultural ecosystem. It is an important source of dietary protein to millions of people living in low-income countries in South-east Asia and Africa. The present study emphasises the development of genomic resources and their application in marker–trait association for plant phenology and yield-related traits in lathyrus. In silico mining of nucleotide sequences identified 203 simple sequence repeat (SSR) motifs, of which trimer repeats (62%) were most abundant followed by tetramer (19%), hexamer (10%), pentamer (6%) and dimer (3%) nucleotide repeats. Of 150 SSR markers screened, 60 markers were amplified 75 alleles from 50 germplasm lines with 2–3 alleles per locus and the polymorphic information content of 0.45 was observed. We report 6 significant marker–trait associations using the developed SSR markers for plant phenology and yield-related traits following mixed linear model (Q+K) analysis. Gene ontology search of trait linked markers revealed marker regions encoding genes related to homeobox-leucine zipper protein ATHB-6-like, rubredoxin family protein, and cationic peroxidise. Understanding the association of novel alleles in trait expression will play a significant role in future lathyrus crop improvement programmes.
Additional keywords: gene flow, genetic improvements, PIC, population structure, putative functions.
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