Genome-wide association reveals novel genomic loci controlling rice grain yield and its component traits under water-deficit stress during the reproductive stage

The decrease in water resources is a serious threat to food security world-wide. In this regard, a genome-wide association study (GWAS) was conducted to identify grain yield and quality-related genes/loci under normal and water-deficit conditions. Highly significant differences were exhibited among genotypes under both conditions for all studied traits. Water-deficit stress caused a reduction in grains yield and an increase in grains protein contents (GPC) and gluten contents (GLC). Population structure divided the 96 genotypes into four sub-populations. Out of 72 significant marker-trait associations (MTAs), 28 and 44 were observed under normal and water-deficit stress conditions, respectively. Pleiotropic loci (RAC875_s117925_244, BobWhite_c23828_341 and wsnp_CAP8_c334_304253) for yield and quality traits were identified on chromosomes 5A, 6B and 7B, respectively, under normal conditions. Under a water-deficit condition, the pleiotropic loci (Excalibur_c48047_90, Tdurum_contig100702_265 and BobWhite_c19429_95) for grain yield per plant (GYP), GPC and GLC were identified on chromosomes 3A, 4A and 7B, respectively. The pleiotropic loci (BS00063551_51 and RAC875_c28721_290) for GPC and GLC on chromosome 1B and 3A, respectively, were found under both conditions. Besides the validation of previously reported MTAs, some new MTAs were identified for flag leaf area (FLA), thousand grain weight (TGW), GYP, GPC and GLC under normal and water-deficit conditions. Twenty SNPs associated with the traits were mapped in the coding DNA sequence (CDS) of the respective candidate genes. The protein functions of the identified candidate genes were predicted and discussed. Isolation and characterization of the candidate genes, wherein, SNPs were mapped in CDS will result in discovering novel genes underpinning water-deficit tolerance in bread wheat.

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Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit

Genetica ◽

10.1007/s10709-016-9932-z ◽

2016 ◽

Vol 144 (6) ◽

pp. 651-664 ◽

Cited By ~ 14

Author(s):

Gabriel Feresin Pantalião ◽

Marcelo Narciso ◽

Cléber Guimarães ◽

Adriano Castro ◽

José Manoel Colombari ◽

...

Keyword(s):

Grain Yield ◽

Association Study ◽

Water Deficit ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

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Short-term water deficit stress induces anthocyanin accumulation and changes in grain yield and yield components in colored rice grain

Agriculture and Natural Resources ◽

10.34044/j.anres.2019.53.3.11 ◽

2019 ◽

Keyword(s):

Grain Yield ◽

Water Deficit ◽

Yield Components ◽

Water Deficit Stress ◽

Rice Grain ◽

Anthocyanin Accumulation ◽

Short Term ◽

Yield And Yield Components ◽

Colored Rice

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Identification and allele mining of new candidate genes underlying rice grain weight and grain shape by genome-wide association study

BMC Genomics ◽

10.1186/s12864-021-07901-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yanan Niu ◽

Tianxiao Chen ◽

Chunchao Wang ◽

Kai Chen ◽

Congcong Shen ◽

...

Keyword(s):

Grain Yield ◽

Association Study ◽

Candidate Genes ◽

Grain Quality ◽

Genome Wide Association Study ◽

Grain Shape ◽

Grain Weight ◽

Genome Wide Association ◽

Rice Grain ◽

Genome Wide

Abstract Background Grain weight and grain shape are important agronomic traits that affect the grain yield potential and grain quality of rice. Both grain weight and grain shape are controlled by multiple genes. The 3,000 Rice Genomes Project (3 K RGP) greatly facilitates the discovery of agriculturally important genetic variants and germplasm resources for grain weight and grain shape. Results Abundant natural variations and distinct phenotic differentiation among the subgroups in grain weight and grain shape were observed in a large population of 2,453 accessions from the 3 K RGP. A total of 21 stable quantitative trait nucleotides (QTNs) for the four traits were consistently identified in at least two of 3-year trials by genome-wide association study (GWAS), including six new QTNs (qTGW3.1, qTGW9, qTGW11, qGL4/qRLW4, qGL10, and qRLW1) for grain weight and grain shape. We further predicted seven candidate genes (Os03g0186600, Os09g0544400, Os11g0163600, Os04g0580700, Os10g0399700, Os10g0400100 and Os01g0171000) for the six new QTNs by high-density association and gene-based haplotype analyses. The favorable haplotypes of the seven candidate genes and five previously cloned genes in elite accessions with high TGW and RLW are also provided. Conclusions Our results deepen the understanding of the genetic basis of grain weight and grain shape in rice and provide valuable information for improving rice grain yield and grain quality through molecular breeding.

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Effect of foliar application of nano iron and manganese chelated on yield and yield component of canola (Brassica napus L.) under waterdeficit stress at different plant growth stages

Agricultural Science Digest - A Research Journal ◽

10.18805/asd.v36i3.11442 ◽

2016 ◽

Vol 36 (3) ◽

Cited By ~ 1

Author(s):

Hossein Zahedi ◽

Leila Pourjafar ◽

Younes Sharghi

Keyword(s):

Grain Yield ◽

Water Deficit ◽

Foliar Application ◽

Harmful Effect ◽

Reproductive Stage ◽

Iron Sulfate ◽

Water Deficit Stress ◽

Growth Stages ◽

Manganese Sulfate ◽

Iron And Manganese

In order to study the effect of nano- iron and manganese fertilizer, a field experiment was conducted at 2013-2014 growing season at the Research Farm in Faculty of Agriculture, Tarbiat Modarres University, Tehran, Iran. Experiment was conducted as a randomized complete block design arrangement in split plot with three replications. Three irrigation regimes (without water deficit stress, water deficit stress at vegetative stage and water deficit stress at reproductive stage) were randomized to the main plots and combinations of foliar nano-iron and nano-manganese application as were randomized to the sub plots. Statistical analysis showed that irrigation and spraying regimes and their interactions had significant effect on most of the measured traits. Water deficit stress significantly reduced yield and yield components of RGS canola variety. The most reduction was observed in plants under water deficit condition at reproductive stage. Use of micronutrients increased canola grain yield. The maximum grain yield was observed in plants that treated with iron sulfate 1 per thousand + manganese sulfate 1.5 per thousand. In general, low concentration levels of iron and manganese foliar application was more effective on plants for reduction harmful effect of water deficit levels than high micronutrient concentrations.

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Effect of Soil Compaction on the Grain Yield of Rice (Oryza sativaL.) under Water-Deficit Stress during the Reproductive Stage

Plant Production Science ◽

10.1626/pps.3.316 ◽

2000 ◽

Vol 3 (3) ◽

pp. 316-322 ◽

Cited By ~ 5

Author(s):

Murshidul Hoque ◽

Tohru Kobata

Keyword(s):

Grain Yield ◽

Water Deficit ◽

Soil Compaction ◽

Reproductive Stage ◽

Water Deficit Stress

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Increase maize productivity and water use efficiency through application of potassium silicate under water stress

Scientific Reports ◽

10.1038/s41598-020-80656-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. A. Gomaa ◽

Essam E. Kandil ◽

Atef A. M. Zen El-Dein ◽

Mamdouh E. M. Abou-Donia ◽

Hayssam M. Ali ◽

...

Keyword(s):

Grain Yield ◽

Water Use Efficiency ◽

Water Deficit ◽

Water Use ◽

Field Experiments ◽

Foliar Application ◽

Potassium Silicate ◽

Water Deficit Stress ◽

Maize Productivity ◽

Use Efficiency

AbstractIn Egypt, water shortage has become a key limiting factor for agriculture. Water-deficit stress causes different morphological, physiological, and biochemical impacts on plants. Two field experiments were carried out at Etay El-Baroud Station, El-Beheira Governorate, Agriculture Research Center (ARC), Egypt, to evaluate the effect of potassium silicate (K-silicate) of maize productivity and water use efficiency (WUE). A split-plot system in the four replications was used under three irrigation intervals during the 2017 and 2018 seasons. Whereas 10, 15, and 20 days irrigation intervals were allocated in main plots, while the three foliar application treatments of K-silicate (one spray at 40 days after sowing; two sprays at 40 and 60 days; and three sprays at 40, 60, and 80 days, and a control (water spray) were distributed in the subplots. All the treatments were distributed in 4 replicates. The results indicated that irrigation every 15 days gave the highest yield in both components and quality. The highly significant of (WUE) under irrigation every 20 days. Foliar spraying of K-silicate three times resulted in the highest yield. Even under water-deficit stress, irrigation every fifteen days combined with foliar application of K-silicate three times achieved the highest values of grain yield and its components. These results show that K-silicate treatment can increase WUE and produce high grain yield requiring less irrigation.

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