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

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.

Identification of QTN and candidate genes for Salinity Tolerance at the Germination and Seedling Stages in Rice by Genome-Wide Association Analyses

“…Emon et al . 21 used rice landraces and found 220 different markers associated with ST, eight of which were sequence-tagged-site markers developed for genes SKC1 , SalT and DST . Using 220 rice accessions, Kumar et al .…”

Abiotic Stress Tolerance in Rice (Oryza sativa L.): A Genomics Perspective of Salinity Tolerance

“…Major findings made in these studies included an observation that distribution of favorable alleles associated with salt tolerance was random in ERCC [53]; 40 new allelic variants found in coding sequences of five salt-related genes [54]; STS marker, RM22418, for SKC1, on Chr. 8 was found associated with salinity tolerance [55]; region containing Saltol was found associated with Na + /K + ratio [56]; marker RM3412 was found associated to salinity tolerance at seedling stage due to its close linkage to SKC gene [58]; and the report that other QTLs, in addition to Saltol, might be involved in salinity tolerance [58]. These reports highlighted that in rice germplasm there might be other genomic regions involved in salt tolerance.…”

“…Association mapping approach is relatively new arrival in plant genetics. There are some reports of association mapping for salt tolerance in rice [13,[53][54][55][56][57][58]. Main findings of these association studies are presented in Table 2.…”

“…Main findings of these association studies are presented in Table 2. In these studies, rice mapping populations used consisted of European Rice Core collection (ERCC) containing 180 japonica accessions [53], 96 rice germplasm accessions including Nona Bokra [55], 220 rice accessions [56], 341 japonica rice accessions [57], 94 rice genotypes [58], and 24 indica rice genotypes [13]. Traits for which data were recorded in these studies included Na + /K + ratio, survival days of seedlings, shoot K + /Na + ratio, Na + uptake, Ca ++ uptake, total cations uptake, Ca ++ uptake ratio, K + uptake ratio, Na + /K + uptake and salinity tolerance scoring.…”

Current Applicable DNA Markers for Marker Assisted Breeding in Abiotic and Biotic Stress Tolerance in Rice (Oryza sativa L.)

“…STS markers were developed based on Insertion/Deletions (InDels) between Nipponbare and 9,311 genome sequences of the previously mentioned gene names. STS markers, Wn11463 and Wn11466, were designed based on 4 bp and 17 bp InDels downstream of SKC1 (LOC_Os01g20160); Wn13900 was based on a 4 bp InDel upstream of SalT (LOC_Os01g24710); Wn13902 and Wn13903 were based on 7 bp and 8 bp InDels in the SalT coding region; Th32637 was based on a 3 bp InDel upstream in DST (LOC_Os03g57240); and Th32638 and Th32369 were based on 12 bp and 18 bp InDels in the coding region of DST (Emon et al 2015). There were some efforts towards breeding salinity tolerance in plant via MAS (Ashraf et al 2012) for the development of salt tolerant cultivars.…”