Novel QTLs affecting rice kernel fissure resistance discovered in the cultivar ‘Saber’ augment those from ‘Cybonnet’

Authors: Pinson, Shannon; Jia, Yulin; Jia, Melissa; GIBBONS, JAMES - University Of Arkansas

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/9/2018
Publication Date: 6/25/2018
Citation: Pinson, S.R., Jia, Y., Jia, M.H., Gibbons, J.W. 2018. Novel QTLs affecting rice kernel fissure resistance discovered in the cultivar ‘Saber’ augment those from ‘Cybonnet’. Crop Science. https://doi.org:10.2135/cropsci2017.10.0593.
DOI: https://doi.org/10.2135/cropsci2017.10.0593

Interpretive Summary: Rice is unique among the cereals for being used primarily for direct human consumption in the form of whole, milled kernels, as opposed to being ground into flour or meal and processed with other ingredients before being eaten by humans. Rice is also typically sold in the U.S. in clear packaging that allows buyers to compare brands and packages for the color, shape, and quality of rice before buying. For this reason, after rice is milled, the broken kernels are separated from the unbroken kernels and sold at lower price to secondary markets, such as rice flour and pet food. The economic value of broken rice is about half that of whole milled rice, so one goal of producers, millers, and rice breeders is to reduce grain breakage during the dehusking and milling processes. One of the primary causes of rice breakage during milling is the formation of cracks (fissures) in the kernels before they enter the mill. A few rice varieties produce grain that is less prone to fissuring than others, and breeders would like to incorporate these fissure resistance (FR) genes into improved rice varieties. Unfortunately, evaluating numerous breeding lines for fissure resistance is laborious even though a laboratory evaluation method can be used, and the environment in which the seed samples were produced can impact results. Use of molecular gene-tags to accomplish breeding via marker-assisted selections (MAS) is particularly desired for traits such as kernel fissure resistance which are environmentally sensitive and costly and laborious to measure. Three genes, or quantitative trait loci (QTLs), for FR were previously discovered in the variety ‘Cypress’, but only one was mapped accurately enough to support MAS breeding. In addition to mapping the other two Cypress FR QTLs more accurately, this study discovered two FR QTLs from a different genetic source, the variety ‘Saber’. Furthermore, it was shown that combining the FR QTLs from both Saber and Cypress provided measurably stronger levels of FR. Sometimes desired genes are associated with non-desirable traits, either through physical linkage of two different genes, or due to a single gene affecting both traits. For example, it has been proposed that thin rice kernels, by virtue of their shape, might be able to distribute adsorbed water in a manner that allows them to resist kernel fissuring. However, thinner rice kernels are not desirable for other reasons. It is therefore notable that this study also showed that FR from either the Cypress or Saber sources was not caused or confounded by kernel shape (length, width, or thickness). This study brought the sum total of FR QTLs available to rice breeders to five, and the molecular markers we identified as linked to the five FR genes can be used by breeders to improve the incorporation of FR into improved rice varieties via MAS.

Technical Abstract: Kernel fissures in rice (Oryza sativa L.) caused by pre- or post-harvest stresses are the leading cause of breakage among milled rice. Such breakage causes economic losses for producers, millers, and marketers. Five QTLs for kernel fissure resistance (FR) were identified among a set of 275 RILs derived from ‘Cybonnet’ x ‘Saber’ (CS-RILs) phenotyped using seven replications of seed harvested from four different environments (years/locations). Use of single nucleotide polymorphisms (SNPs) identified additional polymorphism and allowed for more precise mapping of three FR QTLs previously identified using a limited number of simple sequence repeats (SSRs). Two QTLs were newly discovered in chromosomal regions not previously known to contain genes affecting FR. Saber contributed the FR allele at these newly identified FR QTLs, making them the first FR QTLs not traceable to the ancestral cultivar ‘Cypress’. Fissure resistance among the CS-RILs proved to be independent from (not confounded by) differences for plant height or days to heading, nor with kernel length, width, thickness, or weight. The FR QTLs from Cybonnet and Saber were additive, with stronger levels of FR resulting from pyramiding of FR alleles from both Cybonnet and Saber.