Genetic Architecture of Grain Chalk in Rice and Interactions with a Low Phytic Acid Locus

Authors: Edwards, Jeremy; Jackson, Aaron; McClung, Anna

Submitted to: Field Crops Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/19/2017
Publication Date: 2/21/2017
Citation: Edwards, J., Jackson, A.K., Bryant, R.J., McClung, A.M. 2017. Genetic architecture of grain chalk in rice and interactions with a low phytic acid locus. Field Crops Research. doi:10.1016/jc.fcr.2017.01.015.

Interpretive Summary: Industry and consumers desire rice that once milled produces intact and translucent kernels. The presence of grain chalk, opaque white areas in the rice grain, can reduce milling and cooking quality as well as grain appearance, thus reducing the value of the crop. The presence of grain chalk can be due to the choice of variety and by the environment where the rice was grown. The chalky areas of the grain are due to loosely packed starch granules and small air spaces in the center of the grain that refract light. Environmental and production factors that can cause grain chalk include high temperature stress during grainfilling, low soil fertility, and pest damage. This research was conducted to identify genes which reduce rice grain chalk and were robust across different growing environments. We developed a genetic rice population using a USA cultivar, KBNT LPA, crossed with a cultivar from China, Zhe 733. Both are long grain cultivars and KBNT LPA is translucent, whereas Zhe 733 is chalky. Offspring from the cross were grown in two years and with two planting dates 30 days apart in each year. The objective of the divergent planting dates was to subject the population to extreme differences in temperatures during the grainfill phase. The 187 progeny were harvested at maturity, seed was hulled to produce brown rice, and the grain was evaluated for grain dimensions and grain chalk using an imaging system. The population was also evaluated with 175 genetic markers so that chromosomal regions could be related to grain chalk traits. We identified ten chromosomal regions that accounted for 63.2% of the variation in chalk in the population. The LPA gene which reduces phytic acid in the grain explained 25% of the variation in chalk when present. Independent of this gene, nine other genes, combined, explained 37% of the chalk present indicating that this is a quantitatively inherited trait. Even though the amount of chalk varied to some extent with year and planting date, the genetic markers associated with low chalk were robust across growing environments. These results will benefit breeders that use genetic markers to assist in selection for the development of new varieties that have translucent grain and high economic value.

Technical Abstract: Grain quality characteristics have a major impact on the value of the harvested rice crop. In addition to grain dimensions which determine rice grain market classes, translucent milled kernels are also important for assuring the highest grain quality and crop value. Over the last several years, there has been increasing concern by the rice industry regarding prevalence of chalky grains which are resulting in a loss of some markets. This study was conducted to identify genetic markers associated with grain chalk that could be used by breeders to develop new varieties that have translucent grains across different environments. A mapping population developed from KBNT-1-1, a translucent, low phytic acid (LPA) mutant derived from the US long grain variety Kaybonnet, crossed with Zhe733, a chalky, long grain variety developed in China, was evaluated in replicated trials conducted across two years and two planting dates that differed by one month. The progeny were evaluated for days to flowering and maturity in the field. Grain was harvested at maturity and brown or milled rice were used to determine grain length, width, and percent chalk using an image analysis system. The 187 F12 progeny were evaluated using 174 genome-wide microsatellite markers and one SNP marker, and QTL analysis was performed. A large effect QTL was co-located with the LPA gene, and the mutated KBNT-1-1 LPA allele was associated with increased chalk suggesting that low phytic acid may be one cause of chalk in this cross. Nine additional QTL were detected with the KBNT-1-1 alleles associated with reduced chalk and one with increased chalk. Overlaps were identified between chalk QTL, candidate genes for chalk, and QTL for other agronomic traits. Measures of night time temperature and humidity experienced during grain filling were positively correlated with increased chalk. Year and planting time were shown to also significantly affect chalk. However there was no interaction with the pattern of QTL detected and any of the environmental differences, indicating that these QTL are robust across diverse growing conditions.