Rice Breeding Program, 2013


Rice Experiment Station scientists

Kent S. McKenzie, director

Virgilio Andaya, director of plant breeding: plant breeder, Calrose Medium grains

Farman Jodari, plant breeder, Long grains

Stanley Omar Samonte, plant breeder, Premium Quality and Short grains

Jeffery Oster,
plant pathologist

Cynthia Andaya, research scientist, DNA marker laboratory

The California public rice-breeding program has developed 44 improved rice varieties since accelerated research began in 1969.  Foundation seed of 15 public varieties, one experimental increase, and basic seed of one Japanese premium-quality variety were produced on 161 acres at the Rice Experiment Station (RES) in 2013.

The rice-breeding program consists of five research projects developing California-adapted varieties for specific grain and market types. Virgilio Andaya is responsible for the Calrose medium-grain project and is also director of plant breeding. Stanley Omar Samonte oversees short grains and premium-quality breeding. Farman Jodari leads the long-grain project and also serves as liaison with Southern U.S. breeding programs. Plant pathologist Jeffrey Oster supports efforts to improve disease resistance in all projects. Cynthia Andaya is in charge of the DNA marker laboratory and the grain quality laboratory. Progress highlights from 2013 are reported below.

Breeding nurseries

Seeding of the 2013 breeding nursery began May 2 and was completed May 24. A total of 1,274 crosses were made for rice improvement, bringing the total to 43,824 since 1969. Crosses made in early spring 2013 were grown during the summer at RES to produce second-generation seed.  Crosses made in summer were planted in the Hawaii winter nursery and/or in the RES greenhouse to accelerate the selection process.

The 2013 RES breeding nursery occupied approximately 76 acres.  Water-seeded yield tests included 3,536 small plots and 3,215 large plots. The nursery included about 67,000 water-seeded and 29,580 drill-seeded progeny rows. Second-generation populations from 2011 and 2012 crosses were grown in precision drill-seeded plots on five acres. An estimated 150,000 panicles were selected from various second-generation populations for screening and advancement. Approximately 1,600 headrows of M-402, M-401, Calmochi-101, and 01Y1049 were grown for breeder seed production in 2013.

Selection and harvest of the 2012–2013 Hawaii winter nursery was completed and seed returned to RES for planting in April. The 2013–2014 winter nursery included 9,281 progeny rows planted November 5–7, 2013 and 600 first-generation crosses transplanted December 2, 2013. Selection and harvest was set for March 2014, with seed to be returned for processing and planting in the RES breeding nursery.

The San Joaquin cold-tolerance nursery was planted in cooperation with two local growers.  This seven-acre, drill-seeded nursery included 6,720 rows, and five acres of second-generation populations. Stand establishment and weed control was good. Very little blanking was observed in the rows, but blanking occurred in the second-generation populations.

Statewide yield tests

Statewide yield tests were conducted in grower fields and at the RES in 2013 to evaluate promising advanced selections from all three maturity groups—very early, early, or intermediate-to-late. More detail is reported in the Rice Variety Trials section of this report.

Preliminary yield tests are the initial step of replicated large-plot testing for experimental lines. These tests included 610 entries and check varieties.  Yields of the top experimental lines compared well with check varieties. Superior entries will be advanced to 2014 statewide yield tests.

Calrose medium grains

Calrose medium grains are the cornerstone of California rice production, accounting for most of the state’s total rice acreage. M-202, M-205, and M-206 are the most dominant early-maturing Calrose varieties. 

The “old favorite” M-202 has decreased in acreage because of the increased popularity and acceptability of M-206, released in 2003. M-205 is another high-yielding variety, released in 2000, that is best suited to the warmer areas of the Sacramento Valley.

M-104 is a very early, cold-tolerant variety released in 2000 and is the dominant variety in San Joaquin County and in areas too cold for other varieties. In 2011, the very early M-105 was released as an alternative to M-104. A notable attribute of M-105 is its superior milling yield. It was planted on approximately 14% of Butte County Rice Growers Association acreage and achieved average head rice yield of 68%, outperforming M-205, M-206, and M-104.

Breeding objectives for Calrose varieties continue to be the development of high and stable grain yield, high milling yield, and excellent grain quality, cold tolerance, and disease resistance. This project also is taking steps to improve grain quality and cooking attributes to match the preferences of international markets.

Breeding nursery highlights

The advanced line 08Y3269 performed very well in statewide testing the last four years, outperforming M-202, M-205, and M-206 by 8%, 6%, and 2%, respectively. It is a semidwarf, smooth, early-maturing, Calrose rice derived from a cross made in 2004 with M-205. Compared to M-205, it performed best in Butte and Colusa counties. Number of days to heading was one to two days earlier, with similar seedling vigor and height. In 2013, 08Y3269 was entered into strip trials, where milling samples were taken. Head rice and total milled rice yield were similar to M-205 and M-206. It has slightly larger kernels with less chalk and scored well in resistance to stem rot. Application has been made for foundation seed increase.

Blast resistance

Backcrossing efforts continue to bring different blast resistance genes into M-206. DNA markers facilitate the selection of materials for crossing and generation advance.  In 2013, seven lines were entered into statewide yield tests. Among these lines, 12Y113 yielded better than M-208, with a total grain yield of 9,600 pounds/acre.

A similar strategy to incorporate new sources of blast resistance is being pursued with M-205 and M-105. The goal is to have most medium grains recommended for release to have blast resistance.

Stem rot resistance

Several genes control stem rot resistance. Analysis by the DNA marker lab has identified at least seven chromosomal areas of interest called quantitative trait loci (QTL). The medium-grain project coordinated with the plant pathologist to screen the mapping population for stem rot resistance in an effort to narrow down the regions of interest. Several stem rot-resistant lines were entered in small plots for yield evaluation. Four of these selections scored significantly higher resistance than check varieties M-205, M-206, and M-105. One line, 13P3395, registered a competitive grain yield. These lines will continue to be evaluated.

Mutation breeding

Mutation breeding has been used to generate useful traits in populations derived from M-202, M-206, and M-401. Agronomic performance of M-401 mutants was evaluated in 2013. Further tests will be done to determine if they have maintained the premium quality attributes of M-401.

Long grains

The long-grain breeding project focuses on four major rice types—conventional, jasmine, basmati, and aromatics.  Milling and cooking-quality improvements of conventional long grains and specialty types remain major priorities, followed by resistance to cold-induced blanking and other agronomic and disease-resistance traits.

Conventional long grains

In conventional long grains, extensive cooking-quality screening and selection efforts have eliminated the majority of texture softness from California long-grain breeding material. Consequently, the primary focus is currently on milling yield and cold tolerance.

L-206 is an early-maturing variety with high yield potential released for commercial production in 2006. It is well-adapted to most rice-growing regions of California, except the coldest areas of Yolo and San Joaquin counties. Milling yield of L-206 is 1% to2% lower than L-204. However, recent studies show that L-206 is significantly more resistant to grain fissuring, indicating more stable milling yield at lower harvest moisture. Its cooking and starch characteristics are similar to Southern long grains. Grain yield of L-206 in statewide yield tests averaged 9,220 pounds/acre in 2013. Average yield for M-205 in the same test sites was 9,040 pounds/acre. Average head-rice yield of L-206 during the 2006 through 2013 seasons was 61%.

The long-grain project is seeking to enhance quality and agronomic traits, including milling, cooking qualities, market acceptance, and grain yield. Entries 12Y020 and 11Y1005 performed well in 2013 statewide tests. Of special importance is the performance of these selections in both 2012 and 2013 at the Yolo test location, where they compared favorably with L-206 and M-206. Cooler conditions at the Yolo site have been challenging for many long grains in the past. Both entries are four days later than L-206 and about five inches taller. Milling yields of these lines averaged 3% higher than L-206. Quality evaluations were favorable. Preliminary headrows were planted in the Hawaii winter nursery. Headrow blocks of both lines will be planted in the 2014 nursery at RES.

Specialty long grains

Expanded breeding efforts continued in specialty long grains, including jasmine, basmati, and conventional aromatics such as A-201. Specialty types occupy 50% of the long-grain nursery.

Calmati-202 is a true basmati variety released in 2006. It is an early-maturing, semidwarf, pubescent, aromatic, elongating long grain. Because of its susceptibility to blanking, it is not suited for colder locations. Average yield of Calmati-202 in 2013 early and intermediate-to-late tests was 6,070 pounds/acre, compared to 9,220 pounds/acre for L-206. Calmati-202 is susceptible to fissuring. Thus, timely harvest and proper handling is needed to preserve milling and cooking qualities. Recommended harvest moisture is 19 percent.

Three improved experimental basmati lines—11Y158, 12Y1054, and 13Y135—were tested in 2013 statewide yield tests. Cooking quality evaluations of these lines in earlier generations showed considerable quality advantages over Calmati-202. Line 11Y158 is an early maturing, true basmati type that was in the advanced purification stage in 2013. Average grain yield for 11Y158 over six statewide locations was 4,800 pounds/acre in 2013. This line’s quality improvements include higher cooked-kernel elongation, slender grain shape, and cooked grain texture closer to imported basmati. The primary drawback to 11Y158 is a low milling yield of 36%, compared to 61% for Calmati-202. Experiments are planned for 2014 to identify harvesting and processing procedures to enhance milling yield and cooking quality. Entries 12Y1054 and 13Y135 showed grain and milling yield advantages in 2013 tests. Although these lines yield less than L-206, the current market price differential between basmati rice and standard long grains is more than three to one.

Efforts continued in 2013 on jasmine types through pedigree and mutation breeding. Crosses and backcrosses were made with jasmine material from Southern U.S. breeding programs and foreign introductions. Photoperiod sensitivity of the original Thai jasmine variety Kao-Dak-Mali has been a significant breeding barrier. Pedigree and mutation breeding efforts are generating breeding lines with diverse and unique quality combinations.

In 2013, five jasmine types were tested in statewide yield tests and 50 were in preliminary yield tests. Breeding objectives for jasmine types include low amylose, strong aroma, high degree of whiteness, and smooth cooked grain texture. Entries 12Y1178 and 11Y106 have shown good jasmine quality attributes and acceptable agronomic characteristics.

New variety “A-202”

Aromatic long-grain experimental line 11Y1049 has been approved for release as A-202, a new early-maturing, semidwarf variety.

Compared to A-301, it is nine days earlier, four inches taller, and has significantly higher seedling vigor. The two-year average yield in early statewide tests was 1,800 pounds/acre higher than A-301. Average head-rice yields for the past two years were 60% for A-202 and 53% for A-301.

Both A-202 and A-301 are sensitive to cold-induced blanking and are not recommended for cooler regions. Susceptibility of A-202 to stem rot and aggregate sheath spot is similar to A-201 and A-301.

Milled kernels of this new variety are slightly bolder than A-301. Amylose content, gelatinization temperature type, and starch profile are similar to A-301 and L-206. Subjective evaluations of cooked grain texture indicate that A-202 is slightly softer than L-206.

Areas of adaptation for A-202 include Butte, Yuba, Colusa, Glenn, and Sutter counties. To expedite foundation seed production, a block of breeder seed was grown in the 2012 Hawaii winter nursery. A four-acre foundation field was grown at RES in 2013.

Efforts in conventional aromatics increased in 2013 because of the need for an A-301 replacement with improved agronomic traits. Four experimental lines—11Y1049, 11Y1096, 12Y1128, and 12Y1037—were tested in 2013 statewide yield tests. Entry 11Y1049 was grown as foundation seed in 2013.

Milling quality

Continued improvement in milling yield and stability remains an important objective in the long-grain program. Grain characteristics are being evaluated that will lend milling yield stability under adverse weather, and thus allow a wider window of harvest.

In 2013, all specialty long grains in the preliminary and advanced yield tests were evaluated in special plots for milling yield evaluation. Advanced lines were evaluated at six to eight harvest moistures. Preliminary entries were tested at two harvest moistures. The goal for long grains is to maintain a minimum 64% head-rice yield in advanced breeding lines.

Disease resistance

Stem-rot resistance from the wild species Oryza rufipogon continues to be incorporated into an increasing number of high-yielding, long-grain lines. One entry was tested in statewide tests and 18 were tested in the preliminary tests. Despite a close linkage between the stem rot-resistance trait with increased chalkiness and cold susceptibility, selections are being obtained that have broken this linkage and have a combined low stem-rot score, low blanking, and high milling yield.

Entry 10Y1008 is a stem rot-resistant line that compared favorably with L-206 grain and milling yield in 2013. This line was the most resistant entry in 2013 statewide disease-screening tests. Preliminary yield tests in 2013 also showed record yields, within the long grain nursery, from a number of stem rot-resistant populations.

Short grains and premium quality

The short grain and premium quality project includes conventional short grains, premium-quality short grains, premium-quality medium grains, waxy short grains, low-amylose short grains, and bold grains such as Arborio. Breeding goals emphasize improving grain quality, milling yields, and tolerance to cold temperature, lodging resistance, as well as very-early to early uniform maturity, and resistance to diseases.

Premium quality short grains

Calhikari-202 (CH-202), released as a new short-grain premium quality variety in 2012, continues to show its yield advantage over CH-201 (released in 1999).

In statewide yield tests from 2010 through 2013, CH-202 had higher grain yield than CH-201 in 26 out of 42 test environments. The four-year average was 8,278 pounds/acre, 4% higher than CH-201. Head rice averaged 64% for both varieties the last two years. CH-202 was the higher yielder more frequently at RES, Yolo, and Yuba locations. CH-201 was the higher yielder more frequently in San Joaquin and Colusa test locations. Both were higher yielders on equal occasions in Sutter, Butte, Glenn, and west Sutter test locations.

Five short-grain, premium-quality entries were in the preliminary group of statewide yield tests. Among these, 12Y2167 was noteworthy because of its higher yield, lower lodging, less blanking, and lower chalkiness compared to CH-201 and CH-202.

Premium quality medium grains

Eight premium-quality medium grains were evaluated in 2013 statewide yield tests, two from the advanced group and six in the preliminary group.

One outstanding entry was 11Y2183, which was evaluated in the early and intermediate/late maturity groups. It had significantly higher yields than M-402 in five of seven test locations.

Averaged across the past two years, 11Y2183 yielded 9,480 pounds/acre, which was 15% higher than M-402 and 10% higher than M-401. It had higher whole milled rice yield, similar seedling vigor, earlier heading, less chalkiness, and better taste.

This experimental line will undergo seed increase in 2014.

Conventional short grains

Five conventional short-grain lines were evaluated in 2013 statewide yield tests, two in the advanced group and four in the preliminary group. 

One outstanding entry was 09Y2179, which had significantly higher grain yields than S-102 in three of four test locations.

Averaged across the past two years, 09Y2179 yielded 9,690 pounds/acre, which was 14% higher than S-102. It also had higher whole milled rice yield, higher head-rice percentage, more days to heading, less lodging, and better resistance to sheath spot.

This experimental line was purified in headrows in 2013 and will undergo seed increase in 2014.

Waxy short grains

Three waxy short-grain entries were evaluated in 2013 statewide yield tests. One very promising entry, 09Y2141, was grown in both the very early and early maturity groups. It had higher grain yield than Calmochi-101 (CM-101) and the other two entries.

This line is a high-yielding semidwarf, early maturing, and glabrous. In 2013, 09Y2141 was purified in isolated wet-seeded headrows. In comparison to CM-101, 09Y2141 had significantly higher grain yield in all statewide yield tests from 2010 to 2013. Test locations included Butte, Colusa, RES, San Joaquin, Sutter, Yolo, and Yuba. Yield advantage over CM-101 ranged from 17% to 39%. Grain yield averaged across 27 environments was 10,000 pounds/acre for 09Y2141 and 7,860 pounds/acre for CM-101. This line showed similar seedling vigor, was slightly taller, required two more days to reach heading, and lodged 3% more. It also had a higher head-rice percentage at 65%, larger grain-size dimensions, and lower viscosity when cooked. Blanking was slightly higher in 09Y2141.

External evaluations on cooking quality indicate that 09Y2141 was softer than CM-101 and may be useful for soft mochi and traditional Japanese confectionery.

CM-101, released in 1985, has been the standard waxy short-grain variety.  Because of its favorable evaluation and superior comparison with CM-101, 09Y2141 will undergo foundation seed increase in 2014.

Low-amylose short grains

Two low-amylose short grain lines were evaluated in 2013 statewide tests. Line 09Y2159 was evaluated in the early-maturing advanced group, while 11Y2229 was evaluated in the very early-maturing preliminary group.

Grain yield of 09Y2159 was 8,660 pounds/acre at RES and 8,530 pounds/acre averaged across locations. This was significantly higher than check variety Calamylow-201 (CA-201) at 6,590 pounds/acre at RES and 6,380 pounds/acre across locations. However, its head rice percentage (61%) was lower than that of CA-201 (70%). Seedling vigor also was not as high as CA-201. This line could be used in future crosses with low-amylose short grain lines that have higher head-rice percentage and seedling vigor.

Arborio or bold grains

Arborio or bold-grain rice types are grown on very limited acreage in California. RES has not released a variety of this type. One entry was evaluated in 2013 statewide yield tests. Development of new bold-grain lines could stimulate interest in this type of rice.

Rice Pathology

Breeding for disease resistance is a co-operative effort between plant breeders and the RES plant pathologist.  About 2,566 rows were screened in statewide and preliminary yield tests for stem-rot resistance in 2013.  Since 2005, the immediate backcross program has screened entries for blast, stem rot, and aggregate sheath spot. Advancing generations from crosses have been screened for resistance to both stem rot and aggregate sheath spot (500 rows, with additional greenhouse aggregate sheath-spot screening). In addition, about 4,168 rows derived from breeder crosses have been cycled through the disease nursery to verify disease-resistant lines.

Stem Rot

Screening for stem-rot resistance included about 6,215 rows. Of these, 2,900 rows were drill-seeded, resulting in less seed drift and the establishment of more uniform stands.

In addition, 1,019 rows of a mapping population for identification of stem rot-resistance genes from Oryza rufipogon were evaluated in the field at RES.

Aggregate Sheath Spot

The backcross program aims to transfer aggregate sheath spot-resistance genes into M-206 and L-206. Populations from various backcrosses are being advanced in the greenhouse and in the field nursery. Some lines show resistance equivalent to that found in wild species.


Blast was lower in severity and incidence in both 2012 and 2013. A few affected fields continue to be found, mostly on the west side of the valley. M-104 appears to be more susceptible than other varieties, followed by M-205.

Seedlings of all statewide entries were screened against a mixture of the IG1 and IB1 blast races in the greenhouse for the first time in 2013. This test should confirm the presence or absence of blast resistance genes.

The backcross program also seeks to introduce resistance genes into M-206. Only genes with a wide spectrum of blast resistance in worldwide tests have been chosen. Seven backcrosses were made and screened for blast resistance. In subsequent years, further selections were made with the help of molecular markers. Four of these lines were entered in the early statewide trial in 2012 and 2013. They yielded more than M-208 and even as much as M-206.

Blast infection has been found in some M-208 fields every year since 2009. DNA testing confirmed that a new race of the fungus has been found. This new race is significantly different pathologically from IG1. It is too early to judge whether resistance has been overcome in M-208 since infection occurred in about one in 5,000 to one in 10,000 plants.

A project by the DNA marker lab to screen for blast has been successful. Resistance genes have been pyramided into three lines and are being advanced for agronomic evaluation. These genes were chosen for their broad spectrum and complementary resistance to blast races. The presence of several resistance genes in a variety should prevent rapid loss of resistance when exposed to natural blast fungus populations.

DNA marker laboratory

The DNA marker laboratory supports the different breeding programs and special projects. In 2013, the lab was involved in marker-assisted selection for different grain types, DNA fingerprinting various rice materials, pyramiding of blast resistance genes, genetic mapping of stem rot-resistance genes, herbicide resistance screening, and mutagenesis.

Marker-assisted selection

The main goal of the DNA lab is to help the rice breeders in the selection process, especially with blast resistance and grain quality. In 2013, 4,200 breeding lines were screened for the Calrose project using four blast resistance markers. Approximately 7,300 plants were screened for blast resistance in the short-grain project. About 530 plants from the conventional short-grain project were transplanted in the greenhouse after marker evaluation to recover seeds for use by breeders.

About 2,000 long-grain breeding lines and 152 short grains were evaluated using five DNA markers for grain quality.

Marker-assisted selection for herbicide resistance was done in the laboratory in 2013. About 100 lines were evaluated with markers that detect mutation in the ALS gene that confers resistance to the herbicide imazethapyr (Newpath®) used in Clearfield® rice. The resistant lines identified through this marker work were grown out by plant breeders for further use.

DNA fingerprinting

Another important function of the DNA lab is to assist in variety identity and purity—fingerprinting. A database begun in 2010 now has 177 markers that have been run against 50 rice varieties. Currently, a panel of 11 markers can distinguish California medium grains from each other. A similar panel is in development for short- and long-grain varieties.

The short-grain project requested verification of 42 lines in Calmochi-101 headrows that showed variability in heading days. Using six markers, the lines were confirmed to be Calmochi-101.

In the medium-grain project, about 700 entries were fingerprinted in 2013. These M-202 and M-401 mutants were evaluated using 15 DNA markers.

Variety identification also was conducted on commercial rice to answer seed contamination questions.

Mapping stem-rot resistance

An advanced backcross line from 87Y550/M206*2 has been used to map stem-rot resistance from Oryza rufipogon. Microsatellite markers continue to be added to the genetic map begun in 2010 and field tested to verify stem-rot resistance across seasons and locations. Several genes control stem-rot resistance. DNA segments called quantitative trait loci associated with resistance have been identified.

About 322 lines from a mapping population of M-206 were planted in the field in 2013. Tissues were harvested and DNA extractions performed. Genetic analysis is in progress. The goal of this work is to find a tightly linked marker to stem-rot resistance that can be used by the different breeding projects.

Pyramiding blast resistance

Rice blast disease has the potential to cause considerable damage to rice, although it is not prevalent in California. M-208, which contains a major blast resistance gene, Pi-z, has been observed with blast in some fields.

The backcrossing program aims to incorporate several blast-resistance genes into M-206 background. In 2012, 36 plants out of approximately 6,000 screened second-generation plants were identified with all four resistance genes. This information is now being used by rice breeders in their crossing work.

EMS mutagenesis

Ethyl methane sulfonate (EMS) is one of the most widely used tools for generating mutations in rice breeding. In 2010, the lab started generating materials for the medium- and short-grain projects with this technique. Useful mutants from M-202 and M-401 have been identified with this technology. Some lines will be used for selection to herbicide tolerance. Breeders will evaluate these lines during the 2013 season.