Validation of QTLs in Bangladeshi rice landrace Horkuch responsible for salt tolerance in seedling stage and maturation

Noor, Aftab Uz Zaman; Jewel, G. M. Nurnabi Azad; Haque, Taslima; Elias, Sabrina M.; Biswas, Sudip; Rahman, Md. Sazzadur; Seraj, Zeba I.

doi:10.1007/s11738-019-2963-1

Cited by 6 publications

(11 citation statements)

References 35 publications

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“…The BAAP also includes a number of improved cultivars one of which is the indica cultivar BRRI dhan 47, produced at the Bangladesh Rice Research Institute specifically to be salt tolerant (Mondal et al, 2019). Additionally, seven checks nonaus cultivars were used; two accessions of Pokkali (Bonilla et al, 2002) and one Hor Kuch (Noor et al, 2019) were tolerant checks, while IR 64 (Nakhoda et al, 2012), IR 36 (Rao et al, 2013), IR 29 (Bonilla et al, 2002), and Italica Carolina were susceptible checks. One Pokkali is in the BAAP (written POKKALI here) and the other was sourced directly from the International Rice Research Institute (written Pokkali) as was IR 29 and IR 64.…”

Section: Plant Materialsmentioning

confidence: 99%

Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel

2020

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Salinity is a major abiotic stress which inhibits rice production in coastal, arid and semiaid areas in many countries, such as India and Bangladesh. Identification of salt tolerant cultivars, quantitative trait loci (QTLs) and genes is essential for breeding salt tolerant rice. The aus subpopulation of rice is considered to have originated predominantly from Bangladesh and India and have rich genetic diversity with wide variation in abiotic stress resistance. The objective of this study was to identify QTLs, and subsequently candidate genes using cultivars from the aus subpopulation and compare the results of two different seedling stage screening methods. Salt tolerance at the rice seedling stage was evaluated on 204 rice accessions from the Bengal and Assam Aus Panel (BAAP) grown in both hydroponics and soil under control and salt stress conditions. Ten salt related traits of stress symptoms, plant growth and the content of sodium and potassium were measured. Three cultivars, BRRI dhan 47, Goria, and T 1 showed more salt tolerance than the tolerant check Pokkali in both systems. Genome-wide association mapping was conducted on salt indices traits with 2 million SNPs using an efficient mixed model (EMMA) controlling population structure and kinship, and a significance threshold of P < 0.0001 was used to determine significant SNPs. A total of 97 and 74 QTLs associated with traits in hydroponic and soil systems were identified, respectively, including 11 QTLs identified in both systems. A total of 65 candidate genes were found including a well-known major gene OsHKT1;5. The most significant QTL was detected at around 40 Mb on chromosome 1 coinciding with two post-translational modifications SUMOylation genes (OsSUMO1 and OsSUMO2), this QTL was investigated. The salt tolerance rice cultivars and QTLs/genes identified here will provide useful information for future studies on genetics and breeding salt tolerant rice.

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Section: Plant Materialsmentioning

confidence: 99%

Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel

2020

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“…Here we implemented DArtSeq technique which can genotype a moderate number of SNPs that are well-dispersed in rice genome and aimed to select SNPs close to gene space of the rice genome. In our previous study, we had generated a genetic map on this mapping population by ddRAD technique which failed to capture a significant space of genetic map due to erroneous genotyping and high rate of missing SNP calls (Noor et al , 2019). In this current study, we implemented a robust QTL analysis framework on this improved genetic map and we were able to detect three QTLs for SL and one RL at seedling stage salinity treatment which we could not detect in our earlier study (Supplementary Table 1).…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, in this QTL analysis framework, we applied a linear mixed model to incorporate residual polygenic variation which is a better way to estimate QTL effect for polygenic traits. In our previous study we applied Double digested Restriction Associated DNA (ddRAD) technique to construct genetic map of this population where we failed to map a substantial genetic space (Noor et al , 2019). In this current study, with the aid of an improved genetic map by DArTseq technique and a robust QTL analysis framework we were able to identify additional QTLs with higher likelihood and tighter confidence interval.…”

Section: Introductionmentioning

confidence: 99%

Natural variation in growth and physiology under salt stress in rice: QTL mapping in aHorkuch×IR29mapping population at seedling and reproductive stages

Haque

Razzaque

et al. 2020

Preprint

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3 1 severe due to recent climate changes. To cope with this increased soil salinity, we need to 3 2 develop salt tolerant rice varieties that can maintaining higher yield. Rice landraces indigenous to 3 3 the coastal region of Bangladesh can be a great resource to study the genetic basis of salt 3 4 adaptation. In this study, we developed a reciprocal mapping population between a salt tolerant 3 5landrace Horkuch and a high yielding rice variety IR29. We applied a QTL analysis framework 3 6to identify genetic loci that contributes to salt adaptive responses for two different developmental 3 7 stages of salinity treatment. We identified 14 QTL for 9 traits and found most QTL are unique to 3 8 the specific developmental stage. Moreover, we discovered a significant effect of the 3 9 cytoplasmic genome on the QTL model for some important traits such as leaf total potassium 4 0 and filled grain number. This underscores the importance of considering cytoplasm-nuclear 4 1interaction for breeding programs. Along with that, we detected QTL co-localization for multiple 4 2 traits that highlights the constraint of multiple QTL selection for breeding program. Overall, in 4 3 this study we identified multiple QTL for different physiological and yield related traits for 4 4 salinity treatment for two different developmental stages of the rice plant. We detected a 4 5 significant contribution of cytoplasm-nuclear genome interaction for many traits. This study also 4 6 suggests the selection constraint of donor alleles due to the presence of QTL co-localization. 4 7

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“…In this study, we genotyped a reciprocal mapping population developed from a cross of the salt tolerant landrace, Horkuch and a high yielding variety IR29 by a DArTseq technique 46 , extending earlier work using ddRAD genotyping 47 . Using an improved genetic map and more sophisticated QTL mapping methods, we identified 14 QTLs for 9 traits for salinity treatments at two different developmental stages of the rice plant.…”

Section: Introductionmentioning

confidence: 93%

Salt tolerance QTLs of an endemic rice landrace, Horkuch at seedling and reproductive stages

Haque

Elias

Razzaque

et al. 2022

Sci Rep

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Salinity has a significant negative impact on production of rice. To cope with the increased soil salinity due to climate change, we need to develop salt tolerant rice varieties that can maintain their high yield. Rice landraces indigenous to coastal Bangladesh can be a great resource to study the genetic basis of salt adaptation. In this study, we implemented a QTL analysis framework with a reciprocal mapping population developed from a salt tolerant landrace Horkuch and a high yielding rice variety IR29. Our aim was to detect genetic loci that contributes to the salt adaptive responses of the two different developmental stages of rice which are very sensitive to salinity stress. We identified 14 QTLs for 9 traits and found that most are unique to specific developmental stages. In addition, we detected a significant effect of the cytoplasmic genome on the QTL model for some traits such as leaf total potassium and filled grain weight. This underscores the importance of considering cytoplasm-nuclear interaction for breeding programs. Finally, we identified QTLs co-localization for multiple traits that highlights the possible constraint of multiple QTL selection for breeding programs due to different contributions of a donor allele for different traits.

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Validation of QTLs in Bangladeshi rice landrace Horkuch responsible for salt tolerance in seedling stage and maturation

Cited by 6 publications

References 35 publications

Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel

Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel

Natural variation in growth and physiology under salt stress in rice: QTL mapping in aHorkuch×IR29mapping population at seedling and reproductive stages

Salt tolerance QTLs of an endemic rice landrace, Horkuch at seedling and reproductive stages

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