This project integrates molecular genetics with conventional breeding methods to develop tools and resources for the improvement of rice varieties adapted to California.

The primary emphasis is on the development of molecular DNA markers that can be used to predict the presence or absence of traits of interest, such as disease resistance, cold tolerance, and grain quality.  Use of these markers is intended to accelerate the selection process and to streamline the breeding of improved varieties.

Genes underlying important traits in rice have been identified. The objective of 2009 research was to examine a set of these genes in California rice varieties to determine their usefulness for improving yield and/or quality.

Yield-related genes

Relatively little is known about the genetic basis for high yields. With advances in rice genetics, however, genes that contribute significantly to yield are being isolated and characterized. Some of these genes impact yield by directly affecting grain number (Gn1a gene), grain size (GW2 and GW5 genes), or heading date and plant shape (Ghd7 gene). The studies resulting in the identification of these genes have shown that some higher yielding varieties have specific versions of these genes. The objective of this project is to determine what versions of these genes are present in California varieties and breeding materials. This information can be used to guide the selection of rice germplasm for inclusion into the pool of materials used for breeding.

For the analysis of yield genes, DNA sequencing and DNA marker analysis are being used. To examine the Gn1a, GW2 and Ghd7 genes, DNA sequencing is necessary. Calrose (“ancestral” variety), S-102 (short grain), M-206 (medium grain), and L-202 (long grain) were chosen as representative varieties for initial study. DNA from each variety has been prepared and is undergoing sequencing analysis. The GW5 gene has been shown to impact grain weight and width in some rice cultivars. DNA marker analysis of Calrose, S-102, M-206, and L-202 revealed that only S-102 appears to have the GW5 gene form associated with greater grain width in japonica rices.

A larger set of California varieties has been examined. Most of the ancestral varieties (Colusa, Caloro, CS-M3, CS-S4, and S6) and two of three other short grain varieties (S-101 and S-201, but not S-301) appear to have the same version of the GW5 gene as S-102. Since the GW2 gene also affects grain size, the results of its analysis, along with GW5 results, should provide a more detailed picture of grain size in California rices.

Quality-related genes

Rice starch consists of amylose and amylopectin. Starch is the primary constituent of milled rice and its chemical properties directly affect the cooking, eating, and milling quality of rice grains. The genes involved in starch biosynthesis are well known, and a number of related genetic markers have been used in previous studies.

DNA markers derived from the waxy gene have been used extensively in rice breeding programs. However, waxy gene markers are not able to predict the cooking and eating quality of all rice lines. Other genetic markers may be more useful, so DNA sequencing and/or marker analysis is being done to examine other starch biosynthesis genes in California varieties. Forty-nine cultivars were assessed in 2009. The information generated will be useful in the development of quality markers for the DNA marker lab at the Rice Experiment Station.

Wide-compatibility gene

Cross breeding is the cornerstone of any plant improvement program. The ability of different rice varieties to be crossed and to produce highly fertile offspring is influenced by many genetic factors.

One gene that is a key regulator of fertility and compatibility of indica-japonica rice hybrids is the S5 gene. This gene has recently been isolated and characterized. There are at least three versions of this gene: the japonica, indica, and wide-compatibility versions. Rice varieties with the japonica or indica versions of this gene will produce offspring with poor fertility if crossed with varieties containing the indica or japonica versions, respectively. Rice varieties with the wide-compatibility version of this gene may be crossed with either the japonica or the indica types. These wide-compatibility varieties act as sort of a “bridge” between these two major rice types and may facilitate the transfer of good traits from indica rices to japonica rices that are grown in California and other parts of the U.S.

Initial analysis of 45 California varieties indicates the presence of this wide-compatibility gene in seven cultivars: L-201, L-202, L-203, L-204, L-205, L-206, and A-201.  Additional analysis is under way to determine the presence or absence of this material in the remaining cultivars. The use of varieties containing the wide-compatibility version of the S5 gene or the transfer of this version of the gene into the desired genetic background is an important goal for future breeding efforts, such as the development of hybrid rice.

Priority genes list

In addition to sequencing and marker analysis, a high-priority list of desirable genes is being developed in conjunction with Rice Experiment Station objectives. One target of interest is a seedling coldtolerance candidate gene. Sequence analysis of a gene from M-202 has revealed two genetic markers that may be used to screen germplasm from the USDA rice collection.

Mapping population

In addition to the gene markers analyzed, a recombinant inbred mapping population of 253 lines derived from a cross of L-202/Lemont was also evaluated for genetic diversity. The population was developed by Farman Jodari at the Rice Experiment Station for use in grain quality work.