Abstract
Growing demand for staple crops like rice will need to be achieved predominately through agricultural intensification and more efficient use of inputs. To meet this demand it is essential that the genetic diversity within rice is fully utilized. The aus subpopulation is considered an underappreciated resource within that diversity. A new rice panel, the Bengal and Assam Aus Panel (BAAP) of 266 aus accessions was generated with ∼2 million informative SNPs obtained using skim sequencing at ∼4× depth. The BAAP was grown in the field in Bangladesh in the ‘boro’ season under both continuously flooded and Alternate Wetting and Drying (AWD) irrigation during 2013 and 2014 in Mymensingh and during 2014 in Madhupur. Heading date, grain mass, straw biomass and harvest index were measured. The majority (94%) of BAAP accessions flowered within a relatively small window of 10 days. The AWD irrigation treatment generally caused an increase in grain mass, but no significant genotype by treatment interactions were detected for this trait. Shoot biomass was the only trait that showed evidence of genotype by treatment interaction. The average LD (Linkage Disequilibrium) decay across the genome was 243 Kbp. Genome wide association mapping revealed 115 quantitative trait loci (QTLs). There was little evidence of QTLs specific to the irrigation treatment, and only a few QTLs co-localized with known genes. However, some QTLs were detected across multiple sites and years. These QTLs should be targets for breeding, and include a region around 2.2 Mbp on chromosome 1, a large region in the middle of chromosome 7 and two regions on chromosome 11 (∼10 Mbp and ∼29 Mbp). The BAAP appears to be a valuable addition to the growing collection of GWA mapping populations of rice.
Highlights
Rice (Oryza sativa L.) is one of the world’s most important cereals as it supplies 35–60% of dietary calorie intake for an estimated three billion people (Fageria, 2007; Global Rice Science Partnership [GRISP], 2013)
The aim of this study was to develop an aus panel for genome wide association (GWA) mapping and use it to identify novel genomic loci for yield related traits under continuous flooding (CF) and yield related loci responding to AWD that can be used for breeding
The Bengal and Assam Aus Panel (BAAP) population developed in this study was selected from a larger panel of 511 rice cultivars screened by Travis et al (2015)
Summary
Rice (Oryza sativa L.) is one of the world’s most important cereals as it supplies 35–60% of dietary calorie intake for an estimated three billion people (Fageria, 2007; Global Rice Science Partnership [GRISP], 2013). Developing new management techniques to increase rice yield and breeding of rice varieties that yield more under a range of different environments, including using inputs more sustainably, is a key target to meet these demands. It is estimated that to produce 1 kg of rice 2,500 L of water is required (Bouman, 2009); to produce the average yield of a 4.3 t ha−1 in Bangladesh (Global Rice Science Partnership [GRISP], 2013), a total of 10.75 million liters of water is required per hectare. To reduce the volume of water needed for irrigation during the dry season a number of field management techniques have been developed. Once the water table reaches the required depth below the surface (usually in the range of 15–20 cm below the soil surface) the field is re-flooded and the AWD cycle started. Safe-AWD appears to have no significant impact, or increase grain yield, whereas more severe AWD treatments can result in a significant reduction in grain yield (Carrijo et al, 2017)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
