Identification and mapping of quantitative trait loci (QTL) and epistatic QTL for salinity tolerance at seedling stage in traditional aromatic short grain rice landrace Kolajoha (Oryza sativa L.) of Assam, India

Mazumder, Abhishek; Rohilla, Megha; Bisht, Deepak Singh; Krishnamurthy, S. L.; Barman, Mandira; Sarma, R. N.; Sharma, Tilak Raj; Mondal, Tapan Kumar

doi:10.1007/s10681-020-02602-0

Cited by 16 publications

(6 citation statements)

References 48 publications

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“…Wild rice varieties denote enormous genetic diversity and different molecular functions for many agronomic traits [ 37 ]. For example, only one QTL was major, and 22 QTLs were minor contributing significantly in the phenotypic variation of salt tolerance traits among the rice recombinant inbred lines (RILs) [ 44 ]. However, traditional rice varieties of coastal area in TamilNadu, India are distinct regarding their phenotypic response to salinity.…”

Section: Discussionmentioning

confidence: 99%

Haplotype and diversity analysis of indigenous rice for salinity tolerance in early-stage seedling using simple sequence repeat markers

Mohanavel

Yesudhas

Sharma

et al. 2021

Biotechnology Reports

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Highlights Rice is a staple food for more than three billion people, and rice cultivars have evolved over thousands of years of adaptation to different environmental stresses in different regions. Domestication of rice cultivation led to the diversity of cultivars though phenotypic selection for desirable characters. India is blessed with great diversity of rice germplasm, and these are still conserved for many reasons. The aim of the study was to show the seedling-stage salt tolerance of a total of 50 indigenous rice genotypes from coastal Tamil Nadu, India. Using a hydroponic system, we studied the different agronomic characters from seedling to plant growth hight 14 days after exposure to six different concentrations of saline solution. Rice genotypes showed significant interaction and differential response towards salinity were assessed at the molecular level using simple sequence repeat (SSR) markers linked with salt-tolerance QTL. We found wide genetic distance among the genotypes studied. The combination of morphological findings and molecular assessment revealed better salt-tolerance in a few genotypes. This is, to the best of our knowledge, the first study on the indigenous rice landraces of coastal Tamil Nadu, India.

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Section: Discussionmentioning

confidence: 99%

Haplotype and diversity analysis of indigenous rice for salinity tolerance in early-stage seedling using simple sequence repeat markers

Mohanavel

Yesudhas

Sharma

et al. 2021

Biotechnology Reports

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“…The grouping of landraces and the commonly cultivated varieties together in a group denotes the extent of shared alleles between them. Hence the landraces which are grouped with the cultivars can be used as donors in breeding schemes as they might result in lesser linkage drag (Mazumder et al, 2020). Seven accessions were retained to be admixture.…”

Section: Population Structurementioning

confidence: 99%

Assessing Genetic Diversity and Population Structure of Rice Genotypes using ISSR Markers

Jegadeeswaran,

Nithya,

Salini

et al. 2023

ASD

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Background: The realm of genetic diversity within rice is immense and undermining it provides the opportunity to utilize them in rice improvement programs. Hence in our study, we aimed to undermine the genetic composition and structure of the selected rice accessions utilizing ISSR marker systems. Methods: ISSR analysis encompassed a set of thirty genotypes, comprising 16 cultivated varieties and 14 landraces. The screening was performed with a total of 49 ISSR primers. The consensus tree constructed from banding patterns generated by ISSR-PCR clustered 30 genotypes according to their respective genomes. The Sequential Agglomerative Hierarchical Non-overlapping (SAHN) clustering was employed with the Unweighted Pair Group Method with Arithmetic Averages (UPGMA) method. The grouping of the 30 accessions was carried out through data analysis using NTSYSpc 2.02. Result: Utilizing 49 ISSR markers, the cluster analysis produced three clusters. These clusters displayed pronounced separation and exhibited evident patterns. The Cluster I encompassed Bharathi, BG367-2, PTB33, ASD9, ASD16, ASD20, Rathu Heenati and Columbia-2. Notably, the largest cluster was Cluster II comprising 20 accessions, while Cluster III contained only Jeeraga Samba and Basmati 370. The study validates the efficacy of ISSR markers in detecting polymorphism within and among rice populations and/or species. The resulting DNA profiles hold potential for serving as diagnostic fingerprints of both cultivated and wild rice germplasm, aiding in comprehending evolutionary relationships.

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“…In the QTL analysis of salt tolerance in rice, the permanent populations included recombinant inbred lines (RILs) and introgression lines (ILs). RIL population–parent combinations included Kolajoha×Ranjit [ 12 ], Jiucaiqing× IR26 [ 13 , 14 ], Changbai10×Dongnong425 [ 15 ], Tesanai 2×CB, (Nona Bokra×Pokkali)×(IR4630-22-2-5-1-3×IR10167-129-3-4) [ 16 ], IR4630×IR15324 [ 17 ], Co39×Moroberekan [ 18 ], Milyang23×Gihobyeo [ 19 , 20 ], H359×Acc8558 [ 21 ], IR29×Pokkali B [ 22 ], Yiai1×Lishuinuo [ 23 ], CSR11×MI48 [ 24 ], CSR27×MI48 [ 25 ], and Dongxiang×NJ16 [ 7 ]. IL population–parent combinations included IR64×Tarom Molaii [ 26 ], Ilpumbyeo×Moroberekan [ 27 ], Minghui86×ZDZ057, Minghui86×Teqing Shuhui527×ZDZ057, Shuhui527×Teqing [ 28 ], Lemont×Teqing [ 29 ], Pokkali×IR29 [ 30 , 31 ], Teqing×Oryza rufipogon [ 32 ], Ce258×IR758 62 [ 33 ], Tarome-Molaei×Tiqing [ 34 ], Xiushui 09×IR2061 [ 35 ], IR64×Binam [ 36 ], and Nipponbare×Kasalath [ 37 ].…”

Section: Qtl Analysis Of Salt Tolerance In Ricementioning

confidence: 99%

“…The salt tolerance difference between the parents was small, which was not conducive to the identification of major salt-tolerant sites. Only a few populations were constructed that had salt-tolerant varieties as their parents and used for salt tolerance research, such as Kolajoha×Ranjit [ 12 ], Jiucaiqing×IR26 [ 13 , 14 ], (Nona Bokra×Pokkali)×(IR4630-22-2-5-1-3×IR10167-129-3-4) [ 16 ], IR29×Pokkali [ 22 ], CSR11×MI48 [ 24 ], and CSR27×MI48 [ 25 ].…”

Section: Qtl Analysis Of Salt Tolerance In Ricementioning

confidence: 99%

Gene Mapping, Cloning and Association Analysis for Salt Tolerance in Rice

Fan

Jiang

Meng

et al. 2021

IJMS

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Soil salinization caused by the accumulation of sodium can decrease rice yield and quality. Identification of rice salt tolerance genes and their molecular mechanisms could help breeders genetically improve salt tolerance. We studied QTL mapping of populations for rice salt tolerance, period and method of salt tolerance identification, salt tolerance evaluation parameters, identification of salt tolerance QTLs, and fine-mapping and map cloning of salt tolerance QTLs. We discuss our findings as they relate to other genetic studies of salt tolerance association.

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Identification and mapping of quantitative trait loci (QTL) and epistatic QTL for salinity tolerance at seedling stage in traditional aromatic short grain rice landrace Kolajoha (Oryza sativa L.) of Assam, India

Cited by 16 publications

References 48 publications

Haplotype and diversity analysis of indigenous rice for salinity tolerance in early-stage seedling using simple sequence repeat markers

Haplotype and diversity analysis of indigenous rice for salinity tolerance in early-stage seedling using simple sequence repeat markers

Assessing Genetic Diversity and Population Structure of Rice Genotypes using ISSR Markers

Gene Mapping, Cloning and Association Analysis for Salt Tolerance in Rice

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