Genome-wide association analysis for plant type characters and yield using cgSSR markers in rice (Oryza sativa L.)

Azharudheen, T. P. Muhammed; Nayak, Amrit Kumar; Behera, Sasmita; Kumar, C. T. A.; Marndi, Bishnu Charan; Moharana, Debashis; Singh, Lalan Kumar; Upadhyay, Sameer; Sah, Rameswar Prasad

doi:10.1007/s10681-022-03021-z

Cited by 8 publications

(5 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Similar results were previously reported in rice following the incorporation of multiple genes [2,3,7]. The precise transfer of deficient traits into popular rice varieties by adopting molecular breeding using molecular markers has been accomplished in earlier studies [3,8,19,29,[45][46][47][48]. Ranidhan is a popular variety but is susceptible to submergence caused by flooding, as well as to BB disease.…”

Section: Discussionsupporting

confidence: 73%

Molecular Breeding for Incorporation of Submergence Tolerance and Durable Bacterial Blight Resistance into the Popular Rice Variety ‘Ranidhan’

et al. 2023

View full text Add to dashboard Cite

Ranidhan is a popular late-maturing rice variety of Odisha state, India. The farmers of the state suffer heavy loss in years with flash floods as the variety is sensitive to submergence. Bacterial blight (BB) disease is a major yield-limiting factor, and the variety is susceptible to the disease. BB resistance genesXa21, xa13, and xa5, along with the Sub1 QTL, for submergence stress tolerance were transferred into the variety using marker-assisted backcross breeding approach. Foreground selection using direct and closely linked markers detected the progenies carrying all four target genes in the BC1F1, BC2F1, and BC3F1 generations, and the positive progenies carrying these genes with maximum similarity to the recipient parent, Ranidhan, were backcrossed into each segregating generation. Foreground selection in the BC1F1 generation progenies detected all target genes in 11 progenies. The progeny carrying all target genes and similar to the recipient parent in terms of phenotype was backcrossed, and a total of 321 BC2F1 seeds were produced. Ten progenies carried all target genes/QTL in the BC2F1 generation. Screening of the BC3F1 progenies using markers detected 12 plants carrying the target genes. A total of 1270 BC3F2 seeds were obtained from the best BC3F1 progeny. Foreground selection in the BC3F2 progenies detected four plants carrying the target genes in the homozygous condition. The bioassay of the pyramided lines conferred very high levels of resistance to the predominant isolates of bacterial blight pathogen. These BB pyramided lines were submergence-tolerant and similar to Ranidhan in 13 agro-morphologic and grain quality traits; hence, they are likely to be adopted by farmers.

show abstract

Section: Discussionsupporting

confidence: 73%

Molecular Breeding for Incorporation of Submergence Tolerance and Durable Bacterial Blight Resistance into the Popular Rice Variety ‘Ranidhan’

et al. 2023

View full text Add to dashboard Cite

show abstract

“…Three MQTL identified on chromosome 3 were found to have very low interval and comparatively high weight (Table 2 ), which is advantageous for utilization in strategic breeding programs 35 . The genome-wide association studies carried out on two diverse rice panels did not identify any QTL either for grain weight 36 , 37 or for grain yield 38 on chromosome three owing to population size and marker density used in these studies. Consensus projection of all the minor and major QTL identified in different studies into a single or few MQTL, which explains the variation of all included QTL, signifies the power of meta-QTL identification.…”

Section: Discussionmentioning

confidence: 85%

Understanding complex genetic architecture of rice grain weight through QTL-meta analysis and candidate gene identification

Anilkumar

Sah

Azharudheen

et al. 2022

Sci Rep

Self Cite

View full text Add to dashboard Cite

Quantitative trait loci (QTL) for rice grain weight identified using bi-parental populations in various environments were found inconsistent and have a modest role in marker assisted breeding and map-based cloning programs. Thus, the identification of a consistent consensus QTL region across populations is critical to deploy in marker aided breeding programs. Using the QTL meta-analysis technique, we collated rice grain weight QTL information from numerous studies done across populations and in diverse environments to find constitutive QTL for grain weight. Using information from 114 original QTL in meta-analysis, we discovered three significant Meta-QTL (MQTL) for grain weight on chromosome 3. According to gene ontology, these three MQTL have 179 genes, 25 of which have roles in developmental functions. Amino acid sequence BLAST of these genes indicated their orthologue conservation among core cereals with similar functions. MQTL3.1 includes the OsAPX1, PDIL, SAUR, and OsASN1 genes, which are involved in grain development and have been discovered to play a key role in asparagine biosynthesis and metabolism, which is crucial for source-sink regulation. Five potential candidate genes were identified and their expression analysis indicated a significant role in early grain development. The gene sequence information retrieved from the 3 K rice genome project revealed the deletion of six bases coding for serine and alanine in the last exon of OsASN1 led to an interruption in the synthesis of α-helix of the protein, which negatively affected the asparagine biosynthesis pathway in the low grain weight genotypes. Further, the MQTL3.1 was validated using linked marker RM7197 on a set of genotypes with extreme phenotypes. MQTL that have been identified and validated in our study have significant scope in MAS breeding and map-based cloning programs for improving rice grain weight.

show abstract

“…Submergence reduces the quality and quantity of rice, especially when it occurs during the reproductive and maturity stages. Submergence significantly delays flowering and maturity, reducing grain yield, shoot biomass, harvest index, and yield components (Marndi et al, 2022). Reductions in grain filling, grain number per panicle, and grain weight are primarily responsible for decreased grain production due to submergence (Kato et al, 2014).…”

Section: Impacts Of Submergence On Paddymentioning

confidence: 99%

“…Candidate gene markers can be used to identify genes or QTL for grain production ( Azharudheen et al., 2022 ). Anabolic gene expression requires favorable environmental conditions.…”

Section: Introductionmentioning

confidence: 99%

Physiological and molecular implications of multiple abiotic stresses on yield and quality of rice

et al. 2023

Self Cite

View full text Add to dashboard Cite

Abiotic stresses adversely affect rice yield and productivity, especially under the changing climatic scenario. Exposure to multiple abiotic stresses acting together aggravates these effects. The projected increase in global temperatures, rainfall variability, and salinity will increase the frequency and intensity of multiple abiotic stresses. These abiotic stresses affect paddy physiology and deteriorate grain quality, especially milling quality and cooking characteristics. Understanding the molecular and physiological mechanisms behind grain quality reduction under multiple abiotic stresses is needed to breed cultivars that can tolerate multiple abiotic stresses. This review summarizes the combined effect of various stresses on rice physiology, focusing on grain quality parameters and yield traits, and discusses strategies for improving grain quality parameters using high-throughput phenotyping with omics approaches.

show abstract

Genome-wide association analysis for plant type characters and yield using cgSSR markers in rice (Oryza sativa L.)

Cited by 8 publications

References 70 publications

Molecular Breeding for Incorporation of Submergence Tolerance and Durable Bacterial Blight Resistance into the Popular Rice Variety ‘Ranidhan’

Molecular Breeding for Incorporation of Submergence Tolerance and Durable Bacterial Blight Resistance into the Popular Rice Variety ‘Ranidhan’

Understanding complex genetic architecture of rice grain weight through QTL-meta analysis and candidate gene identification

Physiological and molecular implications of multiple abiotic stresses on yield and quality of rice

Contact Info

Product

Resources

About