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Assessing Trait Contribution and Mapping Novel Qtl for Salinity Tolerance Using the Bangladeshi Rice Landrace Capsule

M. Akhlasur Rahman
PSO
Bangladesh Rice Research Institute

Michael J. Thomson
Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA

Marjorie De Ocampo
International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

James A. Egdane
International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

M. A. Salam
Bangladesh Rice Research Institute, Gazipur 1701, Bangladesh.

M. Shah-E-Alam
Bangladesh Agricultural University, Mymensingh 2202, Bangladesh

Abdelbagi M. Ismail*
International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

Abstract/ Executive Summary:

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 F2:3 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. Out of the 231 F2 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. 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.

Keywords: Novel QTL, Path analysis, Salinity tolerance mechanisms, Salt tolerantindicalandrace, Simple sequence repeats

Location: IRRI Philippines

Start Date: 01-01-2007

End Date: 01-12-2010

Program Area: Variety and Species

Commodity: Rice

Objectives:

The present study aims to (i) establish the relative importance of different traits associated with salinity tolerance and to delineate their importance as individual traits or when combined, ii) identify novel QTL conferring salinity tolerance at seedling stage from the tolerant landrace Capsule using selective genotyping.

Methodology:

The two parents used to develop the mapping population are Capsule and BRRI dhan29. Capsule is an indica landrace tolerant of salt stress at seedling stage and grown in southern coastal region of Bangladesh that are affected by salinity. It is tall (150–155 cm), moderately photoperiod sensitive, produces vigorous seedlings, has long, broad, and droopy leaves, about 6–8 tillers, and with panicle length of 20–25 cm. Grains are typically awnless; bold and blackish in color, with poor grain quality. Its yield is low (1.5–2.0 t ha−1) and mature in 110–115 days (Rahman et al.2016). BRRI dhan29 (BR29)is a high yielding popular indica rice variety with: i)medium stature; 95–105 cm, awnless, with medium slender grains; produce 15–20 tillers and yield 6.0–6.5 t ha−1. It is photoperiod insensitive, but sensitive to salt stress at seedling stage.An F2 population and its F2:3 families were developed and used in this study for mapping traits associated with salinity tolerance

QTL analysis: The 94 selected F2 plants were used for marker analyses and QTL identification representing the two extreme tails of the response distribution. This proportion of selection corresponds to a selection intensity i= 1.14 (Falconer 1989). These progenies were genotyped for 105 SSR and InDel markers separated by an average distance of 11.6 cM. Three analytical approaches were used to identify QTL for salinity tolerance and to estimate their phenotypic effects. First, QTL analysis was per-formed using QGene 4.0 software (Joehanes and Nelson 2008; www.qgene.org), to determine the association be-tween individual marker loci and salt tolerance relatedtraits.To be more precise about the location of the identified QTL for salt tolerance, interval mapping (IM) and composite interval mapping (CIM) analysis were con-ducted. The minimal LOD value required to declare a QTL as significant was obtained empirically from 1000 permutation tests (Churchill and Doerge 1994). The pro-portion of the total phenotypic variation explained by each QTL was calculated as R² value (R²= PVE, phenotypic variation explained by the QTL). Forward cofactor selection method commands were used for the CIM.The proportion of phenotypic variance (R2 value) and additive effects were determined for each trait.The second approach to identify marker-linked QTL was the analysis of distributional extremes. In this method, the 47 salt tolerant families (20.35% of the total)and the 47 salt sensitive families selected as the extreme tails of the F2:3 population were genotyped and the marker-allele frequencies within each class were calculated at all of the 105 marker loci. For unidirectional selective genotyping, the variance of allele frequency for each marker was calculated as a binomial variance(s2q = pq/2N), where p and q are the corresponding allele frequencies at a given marker locus and Nij the number of individuals genotyped at that locus (Falconer1989). Marker allele frequency differences(pr-ps)be-tween the selected salt-tolerant and salt-sensitive progeny families were estimated for each marker locus,where pr is the frequency of the ith allele at the kth marker locus among the salt-tolerant families and ps is the frequency of the ith allele at the kth marker locus among the salt-sensitive families. A trait-based marker analysis (TBA; also known as selective genotyping),which measures differences in marker-allele frequencies between selected classes, was used to identify marker linked QTL (Lebowitz et al.1987; Lander and Botstein1989; Darvasi and Soller1992; Foolad et al.1997). Allele frequency differences were found to be significant when (pr-ps)≥2σp, whereσp=(prqr/2Nr+psqs/2Ns)½ is the standard error of the difference between marker-allele frequencies,Nr is the number of salt-tolerant families,and Ns is the number of salt-sensitive families (Falconer1989; Darvasi and Soller1992; Foolad et al.1997). This test provides a confidence of greater than 95% on the identified QTL (Steel and Torrie1980; Lebowitz et al.1987; Foolad et al.1997).

Source of Information: Rice (2019) 12:63 https://doi.org/10.1186/s12284-019-0319-5

Article Link (Online Journal): https://thericejournal.springeropen.com/track/pdf/10.1186/s12284-019-0319-5

Funding Source:

1. CGIAR

Budget:

Total Budget (Tk.) :

Achievement/Findings:

The overall phenotypic performance under salt stress reflected by visual SES scores is determined by several key traits, including survival, sodium and potassium concentration and rate of growth. Here we used path analysis to assess the genetic contribution of different mechanisms of salinity tolerance during early vegetative stage in the rice landrace Capsule, to identify key factors associated with salt tolerance. The results suggest that selection should be made based on Na+ and K+concentrations and ratios in plant tissue, and seedling survivality fast track the development of improved salt tolerant varieties. Most of the QTL identified here through single marker analysis were also detected using interval map-ping and composite interval mapping, and were further confirmed through graphical genotyping. Several QTL were identified on chromosomes 1 (qNa1.1,qK1.1,qNaK-R1.1,qSur1.1), 2 (qNa2.2), 3 (qSES3.1, qNa3.3,qK3.2, qNaK-R3.3, qSur3.2), 5 (qSES5.2, qNa5.4, qNaK-R5.4) and 12 (qSES12.3, qK12.3, qSur12.3), that are associated with tolerance at seedling stage, and the newly mapped loci on chromosomes 1 and 3 are novel. These QTL are good targets for subsequent fine mapping and cloning to develop gene-based SNP markers. Pyramiding these QTL with previously identified loci will help develop highly tolerant varieties for salt affected areas,especially coastal areas where salt stress is a major impediment for rice production during both dry and wet seasons; an effect further worsening with climate change.

Knowledge Management: Journal