Evaluation of Rice Germplasm under Salt Stress at the Seedling Stage through SSR Markers

Al-Amin, Muhammad; Islam, M. M.; Begum, Shameem Ara; Alam, Mahtab; Moniruzzaman, Md.; Patwary, MM Alam

doi:10.3329/ijarit.v3i1.16093

Cited by 10 publications

(6 citation statements)

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“…This finding is in agreement with earlier findings that wide genetic variation exists for the traits RL and DWsht in rice under saline conditions at the seedling stage (Maiti et al 2006 ; Al-Amin et al 2013 ; Bimpong et al 2014 ). It has also been reported that salinity stress leads to negative root growth and development (Roy et al 2002 ; Rodrigues et al 2002 ).…”

Section: Discussionsupporting

confidence: 93%

Mapping QTLs using a novel source of salinity tolerance from Hasawi and their interaction with environments in rice

Rahman

Bimpong²,

Bizimana³

et al. 2017

Rice

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BackgroundSalinity is one of the most severe and widespread abiotic stresses that affect rice production. The identification of major-effect quantitative trait loci (QTLs) for traits related to salinity tolerance and understanding of QTL × environment interactions (QEIs) can help in more precise and faster development of salinity-tolerant rice varieties through marker-assisted breeding. Recombinant inbred lines (RILs) derived from IR29/Hasawi (a novel source of salinity) were screened for salinity tolerance in the IRRI phytotron in the Philippines (E1) and in two other diverse environments in Senegal (E2) and Tanzania (E3). QTLs were mapped for traits related to salinity tolerance at the seedling stage.ResultsThe RILs were genotyped using 194 polymorphic SNPs (single nucleotide polymorphisms). After removing segregation distortion markers (SDM), a total of 145 and 135 SNPs were used to construct a genetic linkage map with a length of 1655 and 1662 cM, with an average marker density of 11.4 cM in E1 and 12.3 cM in E2 and E3, respectively. A total of 34 QTLs were identified on 10 chromosomes for five traits using ICIM-ADD and segregation distortion locus (SDL) mapping (IM-ADD) under salinity stress across environments. Eight major genomic regions on chromosome 1 between 170 and 175 cM (qSES1.3, qSES1.4, qSL1.2, qSL1.3, qRL1.1, qRL1.2, qFWsht1.2, qDWsht1.2), chromosome 4 at 32 cM (qSES4.1, qFWsht4.2, qDWsht4.2), chromosome 6 at 115 cM (qFWsht6.1, qDWsht6.1), chromosome 8 at 105 cM (qFWsht8.1, qDWsht8.1), and chromosome 12 at 78 cM (qFWsht12.1, qDWsht12.1) have co-localized QTLs for the multiple traits that might be governing seedling stage salinity tolerance through multiple traits in different phenotyping environments, thus suggesting these as hot spots for tolerance of salinity. Forty-nine and 30 significant pair-wise epistatic interactions were detected between QTL-linked and QTL-unlinked regions using single-environment and multi-environment analyses.ConclusionsThe identification of genomic regions for salinity tolerance in the RILs showed that Hasawi possesses alleles that are novel for salinity tolerance. The common regions for the multiple QTLs across environments as co-localized regions on chromosomes 1, 4, 6, 8, and 12 could be due to linkage or pleiotropic effect, which might be helpful for multiple QTL introgression for marker-assisted breeding programs to improve the salinity tolerance of adaptive and popular but otherwise salinity-sensitive rice varieties.Electronic supplementary materialThe online version of this article (10.1186/s12284-017-0186-x) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 93%

Mapping QTLs using a novel source of salinity tolerance from Hasawi and their interaction with environments in rice

Rahman

Bimpong²,

Bizimana³

et al. 2017

Rice

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“…For instance some of the tolerant Saltol ILs had plant height reduction below 20% under salt stress compared to as high as 38% among sensitive lines (Table 3). This result agrees with previous research indicating that an increase in salt stress level causes a reduction in plant height of rice [37]. Salt stress could inhibit cell division directly or indirectly, thus resulting in the leaves and stems of the affected plants becoming stunted [42].…”

Section: Effect Of Salt Stress On Agronomic Traitssupporting

confidence: 94%

“…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. Likewise, a screening of 5000 M4 rice mutant lines from 'IR64' using the SES classification system led to identifying 935 mutant as tolerant; which were further advanced for screening at the reproductive stage.…”

Section: Validation Of Saltol-ils At Vegetative Stagesupporting

confidence: 83%

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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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“…In a range of crops, salinity tolerance at early growth stages often reflects greater tolerance than at later growth stages. For different crops, including tomatoes [ 28 , 29 , 38 ], barley [ 39 ], wheat [ 40 ], maize [ 41 ], cotton [ 42 ], and rice [ 43 ], research has shown that genotypes with enhanced tolerance mechanisms have been selected for their resilience to saline environments at the seedling stage. The aim of our present study was to identify salinity tolerance by phenotyping tomato seedlings using quantitative traits such as reduction in mass of roots and shoots, leaf injury due to salt stress, and tolerance indices derived from dry weights and leaf inorganic ions (K + , Na + , and Ca 2+ ) in order to systematically screen salt-tolerant varieties as well as to understand the biochemical mechanisms of salinity stress tolerance in tomatoes.…”

Section: Discussionmentioning

confidence: 99%

Early Growth Stage Characterization and the Biochemical Responses for Salinity Stress in Tomato

Alam

Tester

Fiene

et al. 2021

Plants

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Salinity is one of the most significant environmental stresses for sustainable crop production in major arable lands of the globe. Thus, we conducted experiments with 27 tomato genotypes to screen for salinity tolerance at seedling stage, which were treated with non-salinized (S1) control (18.2 mM NaCl) and salinized (S2) (200 mM NaCl) irrigation water. In all genotypes, the elevated salinity treatment contributed to a major depression in morphological and physiological characteristics; however, a smaller decrease was found in certain tolerant genotypes. Principal component analyses (PCA) and clustering with percentage reduction in growth parameters and different salt tolerance indices classified the tomato accessions into five key clusters. In particular, the tolerant genotypes were assembled into one cluster. The growth and tolerance indices PCA also showed the order of salt-tolerance of the studied genotypes, where Saniora was the most tolerant genotype and P.Guyu was the most susceptible genotype. To investigate the possible biochemical basis for salt stress tolerance, we further characterized six tomato genotypes with varying levels of salinity tolerance. A higher increase in proline content, and antioxidants activities were observed for the salt-tolerant genotypes in comparison to the susceptible genotypes. Salt-tolerant genotypes identified in this work herald a promising source in the tomato improvement program or for grafting as scions with improved salinity tolerance in tomato.

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Evaluation of Rice Germplasm under Salt Stress at the Seedling Stage through SSR Markers

Cited by 10 publications

References 4 publications

Mapping QTLs using a novel source of salinity tolerance from Hasawi and their interaction with environments in rice

Mapping QTLs using a novel source of salinity tolerance from Hasawi and their interaction with environments in rice

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

Early Growth Stage Characterization and the Biochemical Responses for Salinity Stress in Tomato

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