Next Article in Journal
A Leaf Selfie: Using a Smartphone to Quantify Leaf Vulnerability to Hydraulic Dysfunction
Previous Article in Journal
Prevalent pH Controls the Capacity of Galdieria maxima to Use Ammonia and Nitrate as a Nitrogen Source
Previous Article in Special Issue
Molecular and Morphological Divergence of Australian Wild Rice
Open AccessArticle

In Silico Identification of QTL-Based Polymorphic Genes as Salt-Responsive Potential Candidates through Mapping with Two Reference Genomes in Rice

1
Department of Biotechnology, Faculty of Agriculture and Plantation Management, Wayamba University of Sri Lanka, Makandura, Gonawila, 60170, Sri Lanka
2
Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
3
Department of Botany, Faculty of Natural Sciences, Open University of Sri Lanka, Nawala 11222, Sri Lanka
*
Author to whom correspondence should be addressed.
Plants 2020, 9(2), 233; https://doi.org/10.3390/plants9020233
Received: 27 December 2019 / Revised: 3 February 2020 / Accepted: 5 February 2020 / Published: 11 February 2020
(This article belongs to the Special Issue Genetics in Rice)
Recent advances in next generation sequencing have created opportunities to directly identify genetic loci and candidate genes for abiotic stress responses in plants. With the objective of identifying candidate genes within the previously identified QTL-hotspots, the whole genomes of two divergent cultivars for salt responses, namely At 354 and Bg 352, were re-sequenced using Illumina Hiseq 2500 100PE platform and mapped to Nipponbare and R498 genomes. The sequencing results revealed approximately 2.4 million SNPs and 0.2 million InDels with reference to Nipponbare while 1.3 million and 0.07 million with reference to R498 in two parents. In total, 32,914 genes were reported across all rice chromosomes of this study. Gene mining within QTL hotspots revealed 1236 genes, out of which 106 genes were related to abiotic stress. In addition, 27 abiotic stress-related genes were identified in non-QTL regions. Altogether, 32 genes were identified as potential genes containing polymorphic non-synonymous SNPs or InDels between two parents. Out of 10 genes detected with InDels, tolerant haplotypes of Os01g0581400, Os10g0107000, Os11g0655900, Os12g0622500, and Os12g0624200 were found in the known salinity tolerant donor varieties. Our findings on different haplotypes would be useful in developing resilient rice varieties for abiotic stress by haplotype-based breeding studies.
Keywords: abiotic stress; rice; salinity; whole genome re-sequencing abiotic stress; rice; salinity; whole genome re-sequencing
MDPI and ACS Style

Abhayawickrama, B.; Gimhani, D.; Kottearachchi, N.; Herath, V.; Liyanage, D.; Senadheera, P. In Silico Identification of QTL-Based Polymorphic Genes as Salt-Responsive Potential Candidates through Mapping with Two Reference Genomes in Rice. Plants 2020, 9, 233.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop