Mapping QTLs Related to Salt Tolerance in Rice at the Young Seedling Stage using 384-plex Single Nucleotide Polymorphism SNP, Marker Sets

Bimpong, Isaac Kofi; Manneh, Baboucarr; El-Namaky, Raafat; Diaw, Faty; Amoah, Nana Kofi Abaka; Sanneh, Bakary; Kanfany, Ghislain; Sow, Abdulai; Singh, R. K.; Gregorio, Glenn B.; Bizimana, Jean Berchmans; Wopereis, M.C.S.

doi:10.5376/mpb.2014.05.009

Cited by 17 publications

(23 citation statements)

References 60 publications

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“…Most of the ILs (1738 or 58.9%) had an SES score of 3, while 949 having an SES score of at least 5 were discarded. Similar findings about the variability in salt tolerance among rice cultivars at vegetative stage were previously reported [36]. Al Amin et al [37] observed wide variation by using the SES system to classify 28 accessions from various sources.…”

Section: Validation Of Saltol-ils At Vegetative Stagesupporting

confidence: 82%

“…The observation in our study suggests that in addition to Saltol QTL, some other positive alleles have been transferred to them from the low-yielding donor parent 'FL478'. Beneficial alleles from low-yielding cultivars and wild rice species increased grain yield of rice under abiotic stress, such as salt [36,41], submergence [10] and drought [45]. The effect of salt stress is also reflected on their correlations with grain yield under salt stress, especially with panicle m -2 and grains per panicle (r = 0.53), 1000-grain weight (r = 0.17) and panicle sterility (r = -0.21), thus suggesting the importance of this growth and grain yield traits under salt stress (Table 5).…”

Section: Correlation Of Yield and Other Traitsmentioning

confidence: 99%

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Improving salt tolerance of lowland rice cultivar ‘Rassi’ through marker-aided backcross breeding in West Africa

Bimpong¹,

Manneh²,

Sock³

et al. 2016

Plant Science

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Salt stress affects about 25% of the 4.4 million ha of irrigated and lowland systems for rice cultivation in West Africa (WA). A major quantitative trait locus (QTLs) on chromosome 1 (Saltol) that enhances tolerance to salt stress at the vegetative stage has enabled the use of marker-assisted selection (MAS) to develop salt-tolerant rice cultivar(s) in WA. We used 3 cycles of backcrossing with selection based on DNA markers and field-testing using 'FL478' as tolerant donor and the widely grown 'Rassi' as recurrent parent. In the BC3F2 stage, salt-tolerant lines with over 80% Rassi alleles except in the region around Saltol segment were selected. 429 introgression lines (Saltol-ILs) were identified as tolerant at vegetative stage, of which 116 were field-tested for four seasons at the reproductive stage. Sixteen Saltol-ILs had less yield loss (3-26% relative to control trials), and 8 Saltol-ILs showed high yield potential under stress and non-stress conditions. The 16 Saltol-ILs had been included for further African-wide testing prior to release in 6 WA countries. MAS reduced the time for germplasm improvement from at least 7 to about 4 years. Our objective is to combine different genes/QTLs conferring tolerance to stresses under one genetic background using MAS.

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Section: Validation Of Saltol-ils At Vegetative Stagesupporting

confidence: 82%

Section: Correlation Of Yield and Other Traitsmentioning

confidence: 99%

Improving salt tolerance of lowland rice cultivar ‘Rassi’ through marker-aided backcross breeding in West Africa

Bimpong¹,

Manneh²,

Sock³

et al. 2016

Plant Science

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“…High-throughput SNP genotyping facilities a number of advantages over previous marker systems providing sufficiently dense genome coverage for the dissection of complex traits (Gimhani et al 2016;Takehisa et al 2004;Thomson et al 2011). Bimpong et al (2013) mapped salt tolerant QTL by using 384-plex SNP markers. More recently De Leon (De Leon et al 2016) used 9303 SNP markers generated by genotyping-by-sequencing (GBS) were mapped to 2817 recombination points for salt tolerant QTL identification.…”

Section: Introductionmentioning

confidence: 99%

QTL analysis for rice salinity tolerance and fine mapping of a candidate locus qSL7 for shoot length under salt stress

Jahan

Zhang

et al. 2019

Plant Growth Regul

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Salinity is one of the major abiotic stresses limiting rice production worldwide. Understanding the genetic basis of salinity tolerance is key for rice breeding. In this study, a recombinant inbred line (RIL) population derived from a super hybrid rice Liang-You-Pei-Jiu (LYP9) parents 93-11 and PA64s, exhibited variation in phenotypes including shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), shoot dry weight (SDW), and root dry weight (RDW) under 50 and 100 mM NaCl stress. QTL analysis identified a total of 38 QTLs for these 6 traits under two distinct concentrations of salt, distributing on chromosomes 1, 2, 3, 4, 5, 6, 7 and 10. A total of 21 QTLs were found in 6 stable loci. A novel major QTL, qSL7 for shoot length on chromosome 7 was identified in two distinct concentrations. A chromosome segment substitution line (CSSL) harboring the qSL7 locus from PA64s with 93-11 background was developed and exhibited higher SL value, higher K + concentration, and lower Na + concentration compared to 93-11. With BC 5 F 2:3 derived from CSSL-qSL7/93-11, the qSL7 was fine mapped within a 252.9 kb region on chromosome 7 where 40 annotated genes located including, LOC_Os07g43530, which encodes a DNA-binding domain containing protein reported previously as a transcription factor playing a positive role in salt stress tolerance. Our study provides new genetic resources for improvement of salinity tolerance in rice breeding.

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“…Similarly, none of the other INDELs and SNPs identified in the current study showed strong associations with available salinity ratings. Salinity is not under the control of a single gene; rather, it is controlled by several quantitative trait loci (QTL; Saltol (Mohammadi-Nejad et al, 2008;Thomson et al, 2010) and qDW1.1 in chromosome 1, qDW2.1 and qDW2.2 in chromosome 2, qDW6.1 in chromosome 6 (Bimpong et al, 2014), qSNC3 in chromosome 3, qSNC9 in chromosome 9 and qSNC11 in chromosome 11 (Wang et al, 2012) and rab-16A (Mundy et al, 1990)). Thus, the overall salinity response is a cumulative effect of the responses coming from many QTL/genes.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of genetic diversity of cis-acting elements of Abscisic acid responsive element binding protein (ABRE-BP) in selected Sri Lankan rice varieties

et al. 2017

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Mapping QTLs Related to Salt Tolerance in Rice at the Young Seedling Stage using 384-plex Single Nucleotide Polymorphism SNP, Marker Sets

Cited by 17 publications

References 60 publications

Improving salt tolerance of lowland rice cultivar ‘Rassi’ through marker-aided backcross breeding in West Africa

Improving salt tolerance of lowland rice cultivar ‘Rassi’ through marker-aided backcross breeding in West Africa

QTL analysis for rice salinity tolerance and fine mapping of a candidate locus qSL7 for shoot length under salt stress

Evaluation of genetic diversity of cis-acting elements of Abscisic acid responsive element binding protein (ABRE-BP) in selected Sri Lankan rice varieties

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