Genome-wide association studies using 50 K rice genic SNP chip unveil genetic architecture for anaerobic germination of deep-water rice population of Assam, India

Rohilla, Megha; Singh, Nisha; Mazumder, Abhishek; Sen, Priyabrata; Roy, Priyanka; Chowdhury, Dhiren; Singh, Nagendra; Mondal, Tapan Kumar

doi:10.1007/s00438-020-01690-w

Cited by 30 publications

(24 citation statements)

References 53 publications

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“…The set of 272 rice accessions were genotyped using in-house developed “OsSNPnks” 50K genic Affymetrix chip [ 29 , 30 ] containing a total of 50,051 high-quality SNPs. Alleles for specific SNPs were detected through Axiom Analysis Suite version 2.0 ( https://media.affymetrix.com/ ).…”

Section: Methodsmentioning

confidence: 99%

A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

Hada¹,

Singh²,

Singh³

et al. 2020

PLoS ONE

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Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K "OsSNPnks" genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. The identified SNPs enrich the repository of candidate genes for future markerassisted breeding program to alleviate the damage of RRKN in rice.

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Section: Methodsmentioning

confidence: 99%

A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

Hada¹,

Singh²,

Singh³

et al. 2020

PLoS ONE

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“…In recent studies, 15 AG tolerance loci were detected through GWAS and one candidate gene, a DUF domain-containing protein (LOC_0s06g03520) was identified and found to be highly induced by AG [ 94 ]. Additionally, two candidate genes (LOC_Os03g31550 and LOC_Os12g31350) which encode xanthine dehydrogenase 1 (OsXDH1) and SSXT family protein, respectively, have been identified using GWAS approach [ 96 ]. Nonetheless, the candidate genes currently isolated from rice seedlings for AG do not always overlap in the results of QTL mapping and GWAS.…”

Section: Identification Of Qtls/genes For Ag Tolerancementioning

confidence: 99%

The Molecular Regulatory Pathways and Metabolic Adaptation in the Seed Germination and Early Seedling Growth of Rice in Response to Low O2 Stress

Cen

et al. 2020

Plants

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As sessile organisms, flooding/submergence is one of the major abiotic stresses for higher plants, with deleterious effects on their growth and survival. Therefore, flooding/submergence is a large challenge for agriculture in lowland areas worldwide. Long-term flooding/submergence can cause severe hypoxia stress to crop plants and can result in substantial yield loss. Rice has evolved distinct adaptive strategies in response to low oxygen (O2) stress caused by flooding/submergence circumstances. Recently, direct seeding practice has been increasing in popularity due to its advantages of reducing cultivation cost and labor. However, establishment and growth of the seedlings from seed germination under the submergence condition are large obstacles for rice in direct seeding practice. The physiological and molecular regulatory mechanisms underlying tolerant and sensitive phenotypes in rice have been extensively investigated. Here, this review focuses on the progress of recent advances in the studies of the molecular mechanisms and metabolic adaptions underlying anaerobic germination (AG) and coleoptile elongation. Further, we highlight the prospect of introducing quantitative trait loci (QTL) for AG into rice mega varieties to ensure the compatibility of flooding/submergence tolerance traits and yield stability, thereby advancing the direct seeding practice and facilitating future breeding improvement.

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“…For example, five QTLs for anaerobic germination have been detected on chromosomes 1 (qAG-1-2), 3 (qAG-3-1), 7 (qAG-7-2), and 9 (qAG-9-1 and qAG-9-2) using a backcross population (Angaji et al, 2010). Using GWAS approach, 20 significant genes have been identified contributing to anaerobic germination in rice (Rohilla et al, 2020). Of them, two most relevant genes are OsXDH1, involved in purine catabolism pathway and acting as a scavenger of ROS in plants, and SSXT, which is a GRF1-interacting factor 3.…”

Section: Seed Germinationmentioning

confidence: 99%

Advances in the Identification of Quantitative Trait Loci and Genes Involved in Seed Vigor in Rice

Zhao

Huang

et al. 2021

Front. Plant Sci.

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Seed vigor is a complex trait, including the seed germination, seedling emergence, and growth, as well as seed storability and stress tolerance, which is important for direct seeding in rice. Seed vigor is established during seed development, and its level is decreased during seed storage. Seed vigor is influenced by genetic and environmental factors during seed development, storage, and germination stages. A lot of factors, such as nutrient reserves, seed dying, seed dormancy, seed deterioration, stress conditions, and seed treatments, will influence seed vigor during seed development to germination stages. This review highlights the current advances on the identification of quantitative trait loci (QTLs) and regulatory genes involved in seed vigor at seed development, storage, and germination stages in rice. These identified QTLs and regulatory genes will contribute to the improvement of seed vigor by breeding, biotechnological, and treatment approaches.

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Genome-wide association studies using 50 K rice genic SNP chip unveil genetic architecture for anaerobic germination of deep-water rice population of Assam, India

Cited by 30 publications

References 53 publications

A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

The Molecular Regulatory Pathways and Metabolic Adaptation in the Seed Germination and Early Seedling Growth of Rice in Response to Low O2 Stress

Advances in the Identification of Quantitative Trait Loci and Genes Involved in Seed Vigor in Rice

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