Genome-wide association studies in rice germplasm reveal significant genomic regions for root and yield-related traits under aerobic and irrigated conditions

Padmashree, Revadi; Barbadikar, Kalyani M.; Honnappa,; Magar, Nakul D.; Balakrishnan, Divya; Lokesha, R.; Gireesh, C.; Siddaiah, Anantha M.; Maganti, Sheshu Madhav; Ramesha, Y. M.; Bharamappanavara, Muralidhara; Phule, Amol S.; Senguttuvel, P.; Diwan, J. R.; Subrahmanyam, D.; Sundaram, R. M.

doi:10.3389/fpls.2023.1143853

Cited by 8 publications

(3 citation statements)

References 65 publications

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“…This finding was consistent with the observation from PCA and NJ tree, which also identified three distinct groups. These findings align with the results reported in previous GWAS studies [ 77 , 78 , 79 ]. These sub-populations are thought to arise from allelic sharing, attributed to the accumulation of alleles over time due to spontaneous mutations [ 80 ].…”

Section: Discussionsupporting

confidence: 93%

Discovering New QTNs and Candidate Genes Associated with Rice-Grain-Related Traits within a Collection of Northeast Core Set and Rice Landraces

Roy Choudhury,

Maurya,

Singh

et al. 2024

Plants

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Grain-related traits are pivotal in rice cultivation, influencing yield and consumer preference. The complex inheritance of these traits, involving multiple alleles contributing to their expression, poses challenges in breeding. To address these challenges, a multi-locus genome-wide association study (ML-GWAS) utilizing 35,286 high-quality single-nucleotide polymorphisms (SNPs) was conducted. Our study utilized an association panel comprising 483 rice genotypes sourced from a northeast core set and a landraces set collected from various regions in India. Forty quantitative trait nucleotides (QTNs) were identified, associated with four grain-related traits: grain length (GL), grain width (GW), grain aroma (Aro), and length–width ratio (LWR). Notably, 16 QTNs were simultaneously identified using two ML-GWAS methods, distributed across multiple chromosomes. Nearly 258 genes were found near the 16 significant QTNs. Gene annotation study revealed that sixty of these genes exhibited elevated expression levels in specific tissues and were implicated in pathways influencing grain quality. Gene ontology (GO), trait ontology (TO), and enrichment analysis pinpointed 60 candidate genes (CGs) enriched in relevant GO terms. Among them, LOC_Os05g06470, LOC_Os06g06080, LOC_Os08g43470, and LOC_Os03g53110 were confirmed as key contributors to GL, GW, Aro, and LWR. Insights from QTNs and CGs illuminate rice trait regulation and genetic connections, offering potential targets for future studies.

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Section: Discussionsupporting

confidence: 93%

Discovering New QTNs and Candidate Genes Associated with Rice-Grain-Related Traits within a Collection of Northeast Core Set and Rice Landraces

Roy Choudhury,

Maurya,

Singh

et al. 2024

Plants

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“…Check was significant for all the indices for grain yield under aerobic and irrigated conditions except YRR. We have identified the high yielding rice lines under both aerobic and irrigated field conditions [6].…”

Section: Resultsmentioning

confidence: 99%

Assessment of Multiple Tolerance Indices to Identify Rice Lines Suitable for the Aerobic System of Cultivation

Padmashree

Honappa

Reddy

et al. 2023

IJPSS

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Climate resilience is the most concentrated subject in the current scenario for rice improvement. The aerobic system of rice cultivation involving direct seeding with need-based irrigation in non-puddled soil is gaining ground with respect to a current scenario of water scarcity. The selection of lines suitable and stable under aerobic along with irrigated conditions without any yield penalty is one of the focus areas of the breeding programme for resource use efficiency. In the present study, we have screened a panel of 118 rice lines under aerobic i.e. limited water conditions and irrigated conditions at ARS Dhadesugur Karnataka to identify ideal selection indices viz. STI, TOL, SSI, YSI, YR, YI, PYR, MP and GMP for selecting the best high-yielding and stable lines under both rice cultivation methods. The deployment of selection indices here only pertains to finding the differences in yield per plant under aerobic and irrigated conditions. According to the results of multivariate analysis (correlation and PCA), STI, YI, MP and GMP exhibited a strong correlation with YP and YS. Therefore, they appear to be the most effective stress indices for the selection of lines with good yield potential under water-limited and irrigated conditions. These indices serve as valuable selection criteria for the identification of aerobic-tolerant cultivars from both water-limited and normal conditions. These indices identified lines, DB 5 (Swarna × Oryza nivara (IRGC 81848)) and NPK-40 (Swarna × Oryza nivara (IRGC81832)) wild introgression lines. GNV-14-96-1 (BPT-5204 × Nerica line) Advanced breeding line. JBB 631-1 ((Swarna*2/ IRGC 4105) (RP 5405-JBB-631-1-1-1-1-1-1)) Tropical japonica × indica introgression line. KR-209 (Wazuhophek × ISM) and KR-262 (Wazuhophek × ISM) recombinant introgression lines. TI-36 and TI-124 Ethyl Methane Sulfonate (EMS) mutants of BPT-5204. WB-10 (Langphou) and WB-16 (Phouoibi) North-Eastern Landraces were promising for both environments. These lines are suitable because of low grain yield loss under aerobic conditions and can be further considered for cultivation.

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“…It was also shown that the aminomethyltransferase gene LOC_Os06g04380 was differentially expressed after arsenic treatment (Norton et al, 2008), that peptidyl-prolyl cis/trans isomerase genes have various functions in response to environmental stresses (Ahn et al, 2010), and that LTPL130 was previously selected as a candidate gene located on chr. 8 at 16.86 Mb in a QTL, a QTL for several root and yield-associated traits under aerobic and irrigated conditions (Padmashree et al, 2023). Besides allelic differences between CT and CS rice accessions, another criterion for cold tolerance candidate genes is that their steady-state mRNA levels are up-or downregulated in response to cold temperatures.…”

Section: Cold Tolerance Trait Mappingmentioning

confidence: 99%

Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes

Schläppi,

Jessel,

Jackson

et al. 2023

Front. Plant Sci.

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Due to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate the breeding of climate-resilient cultivars. To uncover genomic regions in rice involved in managing cold stress tolerance responses and to identify associated cold tolerance genes, two inbred line populations developed from crosses between cold-tolerant and cold-sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after 1 week of cold exposure quantified as percent electrolyte leakage (EL) and percent low-temperature seedling survivability (LTSS) after 1 week of recovery growth. This revealed four EL QTL and 12 LTSS QTL, all overlapping with larger QTL regions previously uncovered by genome-wide association study (GWAS) mapping approaches. Within the QTL regions, 25 cold-tolerant candidate genes were identified based on genomic differences between the cold-tolerant and cold-sensitive parents. Of those genes, 20% coded for receptor-like kinases potentially involved in signal transduction of cold tolerance responses; 16% coded for transcription factors or factors potentially involved in regulating cold tolerance response effector genes; and 64% coded for protein chaperons or enzymes potentially serving as cold tolerance effector proteins. Most of the 25 genes were cold temperature regulated and had deleterious nucleotide variants in the cold-sensitive parent, which might contribute to its cold-sensitive phenotype.

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Genome-wide association studies in rice germplasm reveal significant genomic regions for root and yield-related traits under aerobic and irrigated conditions

Cited by 8 publications

References 65 publications

Discovering New QTNs and Candidate Genes Associated with Rice-Grain-Related Traits within a Collection of Northeast Core Set and Rice Landraces

Discovering New QTNs and Candidate Genes Associated with Rice-Grain-Related Traits within a Collection of Northeast Core Set and Rice Landraces

Assessment of Multiple Tolerance Indices to Identify Rice Lines Suitable for the Aerobic System of Cultivation

Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes

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