Molecular Marker-Assisted Rice Improvement, 2013


Project Leader

Thomas Tai, research geneticist, USDA-ARS Crops Pathology and Genetics Research Unit, Dept. of Plant Sciences, UC Davis

The overall objective of this project is to integrate advanced technologies in molecular genetics with conventional breeding methods to develop improved germplasm for the California rice industry.

Primary emphasis is on the development and application of DNA markers to predict the presence or absence of traits of interest, such as disease resistance, cold tolerance, and grain quality.  Use of these markers accelerates the selection process and streamlines the breeding of improved varieties.

Basic genetic studies have resulted in the identification of DNA markers for many important traits. Genes underlying traits for yield, fertility, grain size, grain quality, and others have been identified. The major objectives of 2013 research were (1) to employ next-generation sequencing-based methods to generate highly detailed genetic fingerprints of rice germplasm and to evaluate rice genes present in California varieties, and (2) to continue developing genetic mapping and mutant populations of rice to facilitate trait and gene discovery. Progress toward these objectives is detailed below.

Next–generation genotyping

Two studies were completed and published on the application of the next-generation DNA genotyping method called Restriction Enzyme Site Comparative Analysis (RESCAN) on California varieties and advanced backcross lines exposed to cold stress at the seedling stage of development.

In cooperation with the Rice Experiment Station, 38 entries from the medium-grain and long-grain projects were analyzed with RESCAN. The number of sequence reads for these ranged from 500,000 to 9 million, with an average of 3.8 million. Approximately 7,000 genetic markers were detected over 12 chromosomes. Medium-grain germplasm included M-401 and M-401 mutants in one set and M-206 and M-206 backcross lines with stem-rot resistance in the other set. An analysis of 10 of these lines, including the stem rot-resistance breeding line 87Y550, was conducted using 267 genetic markers. The results of the genotyping of the stem rot-resistant germplasm were consistent with the genetic mapping studies conducted by the Rice Experiment Station.

Genetic analysis of the long-grain advanced backcross lines identified regions that may be associated with stem-rot tolerance. Goals for 2014 research include refinement of the next-generation genotyping pipeline, including improvement of the quality and quantity of sequence data and increasing the capacity for computational analysis of large data sets.


Evaluation of seedling emergence in direct seeded M2036 F6:7. Above, the height of seedlings is plotted on the x-axis against the frequency of recombinant inbred lines on the y-axis. In photo, M-203 (left) exhibits more vigor that M-206.

Rice gene sequencing

A cooperative study with UC Davis colleagues on the application and utility of “exome” sequencing for mutant analysis has been completed. This method selectively sequences the coding regions of the genome.

The goal of this work is to develop markers based on DNA differences within the protein-coding regions of rice genes. Such DNA variation may underlie differences in gene function and contribute to the understanding of important traits.

This study demonstrated the efficacy of exome sequencing for detecting differences in genes due to either induced or natural variation. New laboratory procedures were developed to facilitate more efficient capture of gene DNA for sequencing.

Analysis of sequence data from rice varieties Caloro, Colusa, Lady Wright, Cypress, and M-204 is in progress.

Mapping populations

Progress on mapping populations continues through generation advance and the development of mutant populations.

In 2013, population development work focused on a new mapping population derived from crossing Calmochi-101 and the long-grain breeding line 94Y561. In addition to well-characterized waxy endosperm and pubescence traits, the parental lines also differ in reproductive cold tolerance, stem-rot resistance, and yield. Genetic analysis of these traits is planned.

In the field and in controlled environments, research progressed on the M-2036 population (derived from a cross of M-203 and M-206) consisting of 284 lines. These lines are being genotyped by DNA sequencing. Field observations were consistent with observations made during generation advance. Preliminary analysis shows differences between lines in this mapping population with respect to changes in moisture content over time. Preliminary evaluations of germination, seedling vigor, and reproductive cold tolerance also were performed on a subset of this population. Possible differences in these traits have been detected. More detailed experiments and evaluations of the M-2036 population are planned for 2014.

A population of M-204 mutants was advanced to the third generation to provide seeds for screening and additional experiments. Research in 2013 also included screening the M-204 mutants for an altered response to the herbicide clomazone. Although no resistance was observed, additional screening for useful mutants in this and other traits of value will take place in 2014.