scholarly journals Genome Wide Association Mapping of Grain and Straw Biomass Traits in the Rice Bengal and Assam Aus Panel (BAAP) Grown Under Alternate Wetting and Drying and Permanently Flooded Irrigation

2018 ◽  
Vol 9 ◽  
Author(s):  
Gareth J. Norton ◽  
Anthony J. Travis ◽  
Alex Douglas ◽  
Susan Fairley ◽  
Eduardo De Paiva Alves ◽  
...  
Author(s):  
Caijin Chen ◽  
Anthony J. Travis ◽  
Mahmud Hossain ◽  
Md Rafiqul Islam ◽  
Adam H. Price ◽  
...  

Abstract Key message Identification of a large number of QTL and candidate genes for sodium accumulation in a field grown population of rice derived from theaus subpopulation. Abstract Rice (Oryza sativa L.) is a globally important cereal crop. Sodium (Na+) and potassium (K+) are the major monovalent ions which affect rice growth, and exploring their uptake mechanisms will be useful for understanding rice biology. Since the balance of Na+ and K+ plays a significant role in adaptation of rice to salinity, that biology might inform the search for tolerance. In this study, the Na+ and K+ concentration and Na+/K+ ratio in grains and shoots were analyzed in the Bengal and Assam Aus Panel grown in field conditions under continuously flooded (CF) and alternate wetting and drying (AWD) irrigation. Overall, AWD irrigation significantly reduced the Na+ concentration and increased the K+ concentration in shoots and grains compared to the plants grown under CF. Genome-wide association mapping was conducted on Na+, K+ concentration and Na+/K+ ratio with 2 million SNPs using an efficient mixed model. Only QTLs which contained more than two significant SNPs (p < 0.0001) and where at least one of these significant SNPs passed a 10% false discovery rate were reported. A total of 106 QTLs were identified as being associated with Na+ concentration and Na+/K+ ratio across all traits and field conditions, with 48 QTLs found in multiple traits and/or water conditions. Four notable QTLs (one each on chromosomes 1 and 11, two on chromosome 2) and the haplotype variants of four candidate genes (OsHKT1;5, OsNHX2, LOC_Os02g32490 and OsFAD2_1) are discussed. The QTLs/candidate genes identified here could be useful for breeding rice that accumulates lower concentrations of sodium.


3 Biotech ◽  
2021 ◽  
Vol 11 (5) ◽  
Author(s):  
Kumari Shikha ◽  
J. P. Shahi ◽  
M. T. Vinayan ◽  
P. H. Zaidi ◽  
A. K. Singh ◽  
...  

2017 ◽  
Vol 77 ◽  
pp. 211-218 ◽  
Author(s):  
Jieyun Li ◽  
Awais Rasheed ◽  
Qi Guo ◽  
Yan Dong ◽  
Jindong Liu ◽  
...  

Genomics ◽  
2019 ◽  
Vol 111 (6) ◽  
pp. 1794-1801 ◽  
Author(s):  
Nathanael Fickett ◽  
Andres Gutierrez ◽  
Mohit Verma ◽  
Michael Pontif ◽  
Anna Hale ◽  
...  

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Susan R. McCouch ◽  
Mark H. Wright ◽  
Chih-Wei Tung ◽  
Lyza G. Maron ◽  
Kenneth L. McNally ◽  
...  

Abstract Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.


2017 ◽  
Author(s):  
Ismail Y. Rabbi ◽  
Lovina I. Udoh ◽  
Marnin Wolfe ◽  
Elizabeth Y. Parkes ◽  
Melaku A. Gedil ◽  
...  

ABSTRACTCassava (Manihot esculenta (L.) Crantz) is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Dry matter content and micronutrient density, particularly of provitamin A – traits that are negatively correlated – are among the primary selection objectives in cassava breeding. This study aimed at identifying genetic markers associated with these traits and uncovering the potential underlying cause of their negative correlation – whether linkage and/or pleiotropy. A genome-wide association mapping using 672 clones genotyped at 72,279 SNP loci was carried out. Root yellowness was used indirectly to assess variation in carotenoid content. Two major loci for root yellowness was identified on chromosome 1 at positions 24.1 and 30.5 Mbp. A single locus for dry matter content that co-located with the 24.1 Mbp peak for carotenoid content was identified. Haplotypes at these loci explained a large proportion of the phenotypic variability. Evidence of mega-base-scale linkage disequilibrium around the major loci of the two traits and detection of the major dry matter locus in independent analysis for the white- and yellow-root subpopulations suggests that physical linkage rather that pleiotropy is more likely to be the cause of the negative correlation between the target traits. Moreover, candidate genes for carotenoid (phytoene synthase) and starch biosynthesis (UDP-glucose pyrophosphorylase and sucrose synthase) occurred in the vicinity of the identified locus at 24.1 Mbp. These findings elucidate on the genetic architecture of carotenoids and dry matter in cassava and provides an opportunity to accelerate genetic improvement of these traits.CORE IDEASCassava, a starchy root crop, is a major source of dietary calories in the tropics.Most varieties consumed are poor in micronutrients, including pro-vitamin A.These two traits are governed by few major loci on chromosome one.Genetic linkage, rather than pleiotropy, is the most likely cause of their negative correlation.


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