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Research paper | Open Access

Genetic diversity and association mapping for salinity tolerance in Bangladeshi rice landraces

Reza M. Emona,b,1, Mirza M. Islamb,1( ), Jyotirmoy Halderb, Yeyang Fana( )
Chinese National Center for Rice Improvement/State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
Bangladesh Institute of Nuclear Agriculture, Mymensingh 2202, Bangladesh

1 These authors contributed equally to this work.

Peer review under responsibility of Crop Science Society of China and Institute of Crop Science, CAAS.

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Abstract

Breeding for salinity tolerance using Bangladeshi rice landraces and understand genetic diversity has been limited by the complex and polygenic nature of salt tolerance in rice genotypes. A genetic diversity and association mapping analysis was conducted using 96 germplasm accessions with variable response to salt stress at the seedling stage. These included 86 landraces and 10 indica varieties and lines including Nona Bokra, from southern Bangladesh. A total of 220 alleles were detected at 58 Simple Sequence Repeat (SSR) marker loci randomly distributed on all 12 rice chromosomes and 8 Sequence Tagged Site (STS) markers developed for genes SKC1, DST, and SalT. The average gene diversity was 0.5075 and polymorphism information content value was 0.4426, respectively. Cluster analysis revealed that 68 and 21 accessions were clustered into 2 distinct groups, possibly corresponding to indica and japonica groups, respectively and the remaining 7 landraces were classified as an admixed group. In addition to Wn11463, the STS marker for SKC1, RM22418 on Chr. 8 was significantly associated with salinity tolerance, at the location of a QTL detected in previous studies. Our findings of favorable alleles associated with salinity tolerance in Bangladeshi rice landraces, as well as the development of STS markers for salt tolerance genes, will be helpful in future efforts to breed salinity tolerance in rice.

Keywords

Salinity toleranceSeedling stageSimple sequence repeatOryza sativa LSequence tagged site

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The Crop Journal
Volume 3 Issue 5,
October 2015
Pages 440-444
DOI: 10.1016/j.cj.2015.04.006
Cite this article:
Emon RM, Islam MM, Halder J, et al. Genetic diversity and association mapping for salinity tolerance in Bangladeshi rice landraces. The Crop Journal, 2015, 3(5): 440-444. https://doi.org/10.1016/j.cj.2015.04.006

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Received: 29 January 2015
Revised: 09 April 2015
Accepted: 01 June 2015
Published: 06 June 2015
© 2015 Crop Science Society of China and Institute of Crop Science, CAAS.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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