ARS | Publication request: Genetic variation and association mapping of protein concentration in rice using a germplasm collection

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: February 17, 2012
Publication Date: February 27, 2012
Citation: Bryant, R.J., Jackson, A.K., Yeater, K.M., Yan, W., Fjellstrom, R.G., Mcclung, A.M. 2012. Genetic variation and association mapping of protein concentration in rice using a germplasm collection. Proceedings of the 34th Rice Technical Working Group Meeting, February 27- March 1, 2012, Hot Springs, Arkansas. p.170.

Interpretive Summary: Rice protein is an important source of nutrition and energy for a majority of the world’s population. However, the protein concentration in rice can have an impact on its flavor, texture, cooking and processing quality, thus, affecting its acceptability. It is therefore important to know if genetic markers linked with protein concentration can be identified to help breeders in development of new cultivars. An association analysis for protein concentration in brown rice was performed using a “Mini-Core” set of 200 accessions representative of the germplasm diversity found in the USDA world collection (>18000 accessions) of rice. The accessions were from 14 global regions and contained representatives from O. glaberrima, O. rufipogon, and 5 sub-populations of O. sativa. Protein concentration was determined in replicated trials conducted in two southern states, AR and TX, and analyzed for its association with 165 genome-wide DNA markers. The markers were distributed across the genome approximately every 10 cM. Among the accessions, the average protein concentration ranged from 4.9 % to 11.9 %. The accessions grown in AR had slightly a higher protein concentration then those grown in TX, 5.8 – 11.9% and 4.9 – 11.1%, respectively. Ample variation was seen within each of the rice subpopulations of rice, as well as the 14 geographic regions that the accessions originated from. Accessions from Eastern Europe had the highest level of protein. There was also an effect due to location and accession x location (GxE) interaction demonstrating the importance of assessing protein concentration across multiple environments. Nine markers on eight chromosomes were significantly associated with protein concentration. Three of these markers had been previously reported in other mapping studies. Marker RM125 overlaps a QTL associated with albumin storage proteins (RA5, RA14, and RA17) and is within 0.3 Mb of a predicted prolamin precursor. Marker RM302 is within 1 Mb of GluA-1, a glutelin gene, and marker RM541 is within 1.5 Mb of a predicted prolamin gene. Our results provide germplasm and genetic markers that will assist breeding efforts to develop cultivars that have either high or low protein concentration.

Technical Abstract: Rice protein is an important source of nutrition and energy for a majority of the world’s population. However, the protein concentration in rice can have an impact on its flavor, texture, cooking and processing quality, thus, affecting its acceptability. It is therefore important to know if genetic markers linked with protein concentration can be identified to help breeders in development of new cultivars. An association analysis for protein concentration in brown rice was performed using a “Mini-Core” set of 200 accessions representative of the germplasm diversity found in the USDA world collection (>18000 accessions) of rice. The accessions were from 14 global regions and contained representatives from O. glaberrima, O. rufipogon, and 5 sub-populations of O. sativa. Protein concentration was determined in replicated trials conducted in two southern states, AR and TX, and analyzed for its association with 165 genome-wide DNA markers. The markers were distributed across the genome approximately every 10 cM. Among the accessions, the average protein concentration ranged from 4.9 % to 11.9 %. The accessions grown in AR had slightly a higher protein concentration then those grown in TX, 5.8 – 11.9% and 4.9 – 11.1%, respectively. Ample variation was seen within each of the rice subpopulations of rice, as well as the 14 geographic regions that the accessions originated from. Accessions from Eastern Europe had the highest level of protein. There was also an effect due to location and accession x location (GxE) interaction demonstrating the importance of assessing protein concentration across multiple environments. Nine markers on eight chromosomes were significantly associated with protein concentration. Three of these markers had been previously reported in other mapping studies. Marker RM125 overlaps a QTL associated with albumin storage proteins (RA5, RA14, and RA17) and is within 0.3 Mb of a predicted prolamin precursor. Marker RM302 is within 1 Mb of GluA-1, a glutelin gene, and marker RM541 is within 1.5 Mb of a predicted prolamin gene. Our results provide germplasm and genetic markers that will assist breeding efforts to develop cultivars that have either high or low protein concentration.