Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 7/15/2013
Publication Date: 4/23/2014
Citation: Yan, W., Jackson, A.K., Jia, M.H., Zhou, W., Xiong, H., Bryant, R.J. 2014. Association mapping of four important traits using the USDA rice mini-core collection. In Rice - Germplasm, Genetics and Improvement, Wengui Yan and Jinsong Bao (Ed.). Book Chapter. pp. 105–142. doi: 10.5772/56830. Interpretive Summary: The USDA Rice Mini-Core (URMC) collection has the largest genetic diversity among the reported rice collections, thus is ideal for association mapping. Harvest index is a ratio of grain yield to total biomass, which measures production efficiency. Cultivars high in harvest index are preferred by producers because of high proportion of yield to total products. Grain yield is always the primary objective for rice producers, breeders, scientists, etc. because rice is a staple food to feed half of the world population. Both harvest index and grain yield are complexly inherited and affected by many other traits. Rice sheath blight is the second most damaging fungal disease in rice, especially for high yielding cultivars and in high yielding field environments. Further, sheath blight is a difficult disease to control because resistance is regulated by many genes or quantitative trait loci. Cultivars with high silica content in their hulls would be useful for raw material for silica based industrial compounds, while cultivars with low silica hulls would be more biodegradable and less of a waste problem. Therefore, association mapping studies are conducted by evaluating a diverse array of rice cultivars from around the world and relating the presence of genome-wide genetic markers with variability in plant traits. This chapter summarizes association mapping achievements for these four important traits which will help breeders develop new rice cultivars that will help to feed the world and improve production profitability to benefit growers.
Technical Abstract: Classical quantitative trait loci (QTL) mapping in diploids reveals only a slice of the genetic architecture for a trait because only two alleles that differ between the two parental lines segregate. Association mapping provides an effective method to identify QTL that have effects across a broad spectrum of germplasm. The USDA Rice Mini-Core (URMC) collection was developed using PowerCore software based on 26 phenotypic traits and 70 molecular markers, from 1,794 accessions in the USDA rice core collection that represents genetic diversity among ~20,000 accessions originated from 116 countries in the USDA rice genebank. The URMC was phenotyped for 14 agronomic traits in replicated field trials in Arkansas and Texas during 2009, and genotyped using 155 simple sequence repeat (SSR) markers. Using the genotypic and phenotypic characteristics, genetic analyses proved that the URMC had the largest genetic diversity among the reported rice collections, thus is ideal for association mapping. Subsequently, a series of association mapping studies were conducted to determine harvest index, grain yield, sheath blight resistance and hull silica concentration in the URMC. A total of 36 markers were identified to significantly associate with harvest index and 6 correlated traits; 30 markers were associated with grain yield and 5 correlated traits; 10 markers were associated with sheath blight resistance, and 4 markers were associated with hull silica concentration.