Assessing trait contribution and mapping novel QTL for salinity tolerance using the Bangladeshi rice landrace Capsule

Abstract

Background Salinity is one of the most widespread abiotic stresses affecting rice productivity worldwide. The purpose of this study was to establish the relative importance of different traits associated with salinity tolerance in rice and to identify new quantitative trait loci (QTL) conferring tolerance to salinity at seedling stage. A total of 231 F 2:3 plants derived from a cross between a sensitive variety BRRI dhan29 (BR29 hereafter) and Capsule, a salt tolerant Bangladeshi indica landrace, were evaluated under salt stress in a phytotron. Results Out of the 231 F 2 plants, 47 highly tolerant and 47 most sensitive lines were selected, representing the two extreme tails of the phenotypic distribution. These 94 plants were genotyped for 105 simple sequence repeat (SSR) and insertion/deletion (InDel) markers. A genetic linkage map spanning approximately 1442.9 cM of the 12 linkage groups with an average marker distance of 13.7 cM was constructed. QTL were identified on the long arm of chromosome 1 for Na + concentration, K + concentration, Na + -K + ratio and survival; chromosome 3 for Na + concentration, survival and overall phenotypic evaluation using the Standard Evaluation system (SES); and chromosome 5 for SES. A total of 6 pairwise epistatic interactions were also detected between QTL-linked and QTL-unlinked regions. Graphical genotyping indicated an association between the phenotypes of the extreme families and their QTL genotypes. Path coefficient analysis revealed that Na + concentration, survival, Na + -K + ratio and the overall phenotypic performance (SES score) are the major traits associated with salinity tolerance of Capsule. Conclusions Capsule provides an alternative source of salinity tolerance aside from Pokkali and Nona Bokra, the two Indian salt tolerant landraces traditionally used for breeding salt tolerant rice varieties. Pyramiding the new QTL identified in this study with previously discovered loci, such as Saltol , will facilitate breeding varieties that are highly tolerant of salt stress. Electronic supplementary material The online version of this article (10.1186/s12284-019-0319-5) contains supplementary material, which is available to authorized users.

Mapping quantitative trait loci for disease resistance to false smut of rice

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Genetic Map Construction and Functional Characterization of Genes within the Segregation Distortion Regions (SDRs) in the F2:3 Populations Derived from Wild Cotton Species of the D Genome

“…A study conducted on determining signi cant QTLs for drought stress tolerance, majority of the marker loci co-localized with known QTLs for blast tolerance or NBS-LRR disease resistance genes were located within the regions of signi cantly distortion levels (Dixit et al 2014). Similar observation on Bangladeshi rice landrace Capsule in relation to salt stress tolerance (Rahman et al 2019). The four parental lines used in the construction of the genetic map are known to contain traits for resistance to bacterial blight (G. davidsonii), sucking pests such as aphids (G. klotzschianum), Fusarium wilt, silver leaf white y and cotton bollworm resistance (G. thurberi), Verticillium wilt (G. trilobum).…”