Rice Breeding Program - 2007




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Project Leader and Principal  Investigators

Kent S. McKenzie, Director

Farman Jodari, plant breeder, long grains

Carl W. Johnson, plant breeder, Calrose medium grains

Jacob Lage,
plant breeder, Clarose medium grains

Virgilio Andaya, plant breeder, Premium quality and short grains

Jeff Oster, rice pathologist




The California public rice-breeding program has developed 42 improved rice varieties since accelerated research began in 1969. Foundation seed of 15 public varieties and basic seed of two Japanese premium--quality varieties were grown on 170 acres at the Rice Experiment Station (RES) in 2007. Two years of voluntary and aggressive testing of RES foundation seed found no evidence of the Liberty Link® trait discovered at trace levels in Southern U.S. long-grain rice. Extensive testing by the California Rice Commission of commercial rice seed also has been negative for this trait that has never been reported in any commercial rice grown in California.

The rice-breeding program consists of four ongoing research projects developing California-adapted varieties for specific grain and market types. Jacob Lage is replacing Calrose medium-grain plant breeder Carl Johnson after his many years of service at RES. Virgilio Andaya is the new project leader for premium quality, waxy, and California short grains. He also brings expertise in DNA marker technology. Progress highlights from 2007 are reported below.

Breeding nurseries

Seeding of the 2007-breeding nursery was more “normal” than in the previous two seasons, running May 15-25. Statewide average yields were 8,220 pounds/acre, according to USDA statistics.

A total of 1,253 new crosses were made for rice improvement, bringing the total to 34,808 since 1969. Crosses made in early spring 2007 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 greenhouse to accelerate the selection process.

The 2007 RES breeding nursery occupied approximately 80 acres. Water-seeded yield tests included 3,888 small plots and 3,668 large plots. Small seed-increase plots and cooking samples were grown on 2.5 acres and included 40 advanced breeding lines. Sixty-seven experimental lines in 4,520 headrows were grown for seed increase, quality evaluations, and purification.

The nursery included 54,000 water-seeded and 4,000 drill-seeded progeny rows. Selections were made for approximately 10,000 progeny rows. Second generation populations from 2005 and 2006 crosses were grown in precision drill-seeded plots on 20 acres. An estimated 200,000 panicles were selected from various second-generation populations for screening and advancement. Approximately 2,800 headrows of M-104, M-205, M-206, Calmochi-101, Calmati-201, Calmati-202, and L-206 were grown for breeder seed production.

The 2006-7 Hawaii winter nursery included 8,460 progeny rows and a first-generation nursery of 550 crosses. The 2007-8 winter nursery, also with 8,460 rows, was planted November 4th and 5th. First-generation plants from 570 crosses were transplanted to the nursery between December 6th and 8th. Selection and harvest was scheduled for April 2008, with seed to be planted at RES by late spring.

The 2007 cold-tolerance nursery at UC Davis contained 7,800 second-generation, drill-seeded progeny rows. Second-generation, drill-seeded populations were also grown on four acres in Yolo County. The nursery suffered heavy bird damage but some selections were made.

The cold tolerance nursery in San Joaquin County was planted in the fields of two cooperating growers. This five-acre, drill-seeded nursery included 11,500 rows and 3.6 acres of second-generation populations. In addition, a large-plot, single-replication yield test of 64 medium-grain lines grown in cooperation with UC provided a good opportunity to screen for blanking-resistant material.

Statewide Yield Tests

Statewide yield tests were conducted in grower fields and at RES in 2007 to evaluate promising advanced selections from all three maturity groups – very early, early, or intermediate-to-late. Entries that performed well advanced for further testing. More detail is reported in the Variety Trials section of this annual report.

Preliminary yield tests are the initial step of replicated large-plot testing for experimental lines. These tests included 966 entries and check varieties. Yields of top experimental lines compare well with check varieties. Superior entries advanced to 2008 statewide yield tests.

Calrose medium grains

Calrose medium grain breeding focuses on high-yield potential, resistance to lodging and disease, seedling vigor, improved milling yields, and resistance to cold temperature blanking. Efforts begun in 1996 resulted in the release of two blast-resistant varieties – M-207 and M-208.

In 2007, M-208 was grown on approximately 600 acres in western Colusa County, where blast had been previously observed. No blast was reported in M-208 fields last year. M-208 yielded equal to M-202 but less than M-205 fields not affected with blast. Other grower observations include less lodging than M-202 and milling equal to or slightly higher than M-202. Most growers said they would plant M-208 again and probably increase their acreage. M-208 is adapted to the majority of the M-202 growing areas and provides a valuable alternative for growers who may need to manage for the presence of blast.

Lower harvest moisture is another important selection objective. In 2007, 97% of 37 first-time entries in statewide yield tests showed 1-2% lower harvest moisture. Their heading dates were in the range of other Calrose medium grains.

Selection for improved lodging resistance, seedling vigor, and milling yield continues. Fifteen of 37 new entries in statewide yield tests had one to two points more head rice than high-performing checks.

Experimental lines 05-Y-724 and 05-Y-471 are two promising very early, smooth, high-yielding entries in the second year of statewide tests. 05-Y-724 yield ranked first the last two years. It appears better adapted to warmer areas. The other line, 05-Y-471, appears better suited to cooler regions. Two other high-yielding, very early entries – 06-Y-239 and 06-Y-889 – also show promise and are being advanced.

Forty-nine Calrose medium grain entries from 2007 yield tests were grown in preliminary yield tests in the Hawaii winter nursery. Maturities range from M-104 to M-205. These entries have greater yield potential than their respective highest-yielding checks. Their lodging resistance is superior to M-202 and head rice is one to two points higher. Some new entries with blast resistance yielded 11-30% more than M-206 or M-205. Chinese crosses have produced excellent yields.

Eleven blast-resistant entries were evaluated; two of them will be retested in 2008. Altogether, there are now 51 entries with blast resistance yielding more than the average of all checks. Selected entries range from M-104 to M-202 maturities. Each generation of new blast materials shows increases in resistance to blanking and improved head rice. Yield advantages could translate to 4-6% in the field. More yield tests are planned for 2008.

No breeding research was conducted on transgenic herbicide resistant M-202 or on Clearfield® rice in 2007.

Milling quality tests included 558 entries in 2007. Sixty-one of the 185 saved entries had head rice yields similar to the best Calrose check. The current standard bearers are M-103, M-206, and M-205. Twenty-one of 63 advancing blast entries had head rice equal to or better than their respective check. Also, milling samples from seed-increase fields and advanced experimental plots were evaluated at grain moistures ranging from 25 percent to 17 percent to determine average head and total milled rice.

Milling data also showed that M-206 between 20-23% field moisture remains stable for four to five days before continuing dry down. Another study showed that M-206 maintained head rice at a wide range of harvest moisture, even as low as 15%. If verified with more testing, this could allow growers to harvest at lower moisture and reduce drying costs.

Stem rot resistance for Calrose medium grains remains a top priority. Current stem rot-resistant lines 07-Y-232, 07-Y-255, and 07-Y-381 have excellent yields compared to M-206; however, their resistance scores are only slightly better. Yields are 20-32% better than the long-grain resistance check. These entries have earlier maturity and improved milling yield and adaptation.

In 2005 a germplasm discovery was made that could allow rice to be grown in 8-inch (or deeper) water and thus holds potential as another weed control tool. This natural mutant was derived from M-206 and has been designated “DW-206.” Encouraged by results from 2006, testing expanded in 2007. Yields were 500 pounds/acre less than M-206 but 600 pounds/acre more than M-202. Head rice was comparable.

Progress continues to be made on improved straw strength in experimental lines with lodging resistance better than M-204. Resistance to low-temperature blanking continues to be screened in the RES refrigerated greenhouses and in cool growing regions. Fifty-nine experimental entries were grown in a special drill-seeded, large-plot yield test in San Joaquin County and screened for cold tolerance.

Long grains

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

L-206, a conventional long-grain with firmer grain texture and better starch characteristics than L-204, was released for commercial production in 2006. Its primary advantages are improved cooking quality, higher grain yield, and earlier maturity. Milling yield is slightly lower than L-204.

L-206 is a very early to early-maturing semidwarf. Average heading date is four days earlier and plant height is slightly shorter than L-205 and M-202. Lodging potential is similar to L-205, but it may lean with excessive dryness at harvest. Susceptibility to cold-induced blanking and to rice diseases is similar to L-205 and M-202.

Grain yield of L-206 averaged over eight seasons has been significantly higher than M-202 at RES and similar to L-205 and M-202 at an eastern Sutter location. Average yields were 8,890 pounds/acre at the cooler Sutter site and 10,170 pounds/acre at RES. Yields from Yolo and San Joaquin locations were not competitive with M-202. In 2007, however, L-206 yield was second at 9,850 pounds/acre in a drill-seeded San Joaquin test.

Three-year average yields at the Butte site were 8,770 pounds/acre for L-206 and 7,810 pounds/acre for M-202. Yield tests for three years at additional locations were not significantly different from each other. In 2007, L-206 yielded competitively with other varieties, including medium grains. It should be adapted to most rice-growing regions except the coolest locations of Yolo and San Joaquin counties. The six-year, head-rice yield averaged nearly 63%, comparable to L-205.

Other promising conventional long grains are being evaluated in detail. DNA markers were successfully used in 2007 to determine amylose synthesis genes in 1,200 long-grain breeding lines. Part of a collaborative project with UC Davis and USDA, the DNA analysis system at the Rice Experiment Station is proving to be a valuable tool for plant breeders.

Breeding efforts increased in specialty long grains – jasmine, basmati, and conventional aromatics such as A-201.

Calmati-202, a true basmati, was released in 2006. Cold-induced blanking is a problem with this variety. Calmati-202 has shown significantly lower yield potential than L-205 and M-202 in statewide yield tests, averaging just 6,740 pounds/acre. Grain and cooking quality is superior to Calmati-201. It has finer grain shape and thus lower yield potential. Calmati-202 is not intended as a replacement for conventional aromatic varieties. Because of its susceptibility to fissuring at low harvest moisture, proper handling is important to preserve milling and cooking qualities. Recommended harvest moisture is 18%.

A new series of basmati selections with improved cooking quality advanced in statewide trials in 2007. Entries 06-Y-152 and 06-Y-154 possess true basmati qualities that are nearly indistinguishable from imported basmati types. Their primary features are higher elongation, flakier texture, and minimal curving of cooked grains. Appearance of the cooked rice is very important to basmati consumers. Both grain and milling yield are lower than Calmati-202. Further testing is under way.

Efforts also continued in 2007 to breed improved jasmine types through pedigree and mutation breeding. Twenty-four advanced jasmine selections were tested in 2007.

Milling quality is another focus of long-grain improvement. Grain characteristics are being selected that will lend milling yield stability to long-grain lines under adverse weather conditions to allow a greater period of harvest. Efforts to enhance milling quality include screening advanced lines for resistance to grain fissuring. Milling yield potential of 30 advanced long-grain lines in statewide yield tests was also evaluated.

RES is participating in a cooperative project with USDA – “RiceCAP” – to apply genomic discoveries to improved milling quality and disease resistance in rice. Arkansas, California, Louisiana and Texas are pooling knowledge gained from genetic research. RES contributed results of fissuring studies from three milling populations and a long-grain milling quality population for developing molecular markers associated with milling quality. Initial results indicate clear and consistent differences among progeny and parents of this population.

Stem rot resistance from the wild species Oryza rufipogon has been transferred to a number of high-yielding, long-grain lines. Thirty-five entries with a range of stem rot resistance were tested in 2007 statewide yield tests. A few entries continue to show significant improvement – low stem rot scores, low blanking, early maturity and high yield potential.

Premium quality & short grains

The short-grain and premium-quality, rice-breeding program is in transition with the hiring of Virgilio Andaya as new project leader in 2007. Priorities are building on previous progress. This project includes conventional short grains, premium quality short grains, premium quality medium grains, waxy short grains, low-amylose short grains, and bold grains like the Arborio type. Progress toward breeding goals that include premium grain quality, high yield potential, disease resistance and adaptation to cold environments are being assisted by greater use of DNA marker technology now at RES.

About 20% of all breeding lines in this project are conventional short grains. S-102 is still the dominant variety in commercial production because of its high-yield potential and very early maturity, resistance to cold-induced blanking, and large kernel size. This variety is susceptible to stem rot, however, and is pubescent (rough leaves and hulls). The goal is to capture favorable characteristics of this variety and incorporate stem rot resistance and smooth hulls. In 2007, 12 lines were tested in preliminary yield tests at RES and may be advanced to statewide yield tests, pending grain quality evaluation and taste tests.

Development of premium quality short and medium grain rice varieties accounts for about 60% of this project. Premium quality is a term used to identify California medium grains like M-401 and the Japanese varieties Koshihikari and Akitakomachi. Grain quality is perceived differently by different cultures – a difficult challenge for rice breeders.

Calhikari-201 is the first variety of this type developed in and for California. It was derived from a cross involving Koshihikari and S-101. Released in 1999, it has been high yielding, early maturing, of good seedling vigor, and is lodging resistant. However, it has a rough hull, is susceptible to stem rot and blanking, and its grain quality does not equal Koshihikari. Breeding efforts are focused on improved grain quality and agronomic attributes.

In 2007, 12 premium-quality short grains were in statewide yield tests. Four of those entries have been tested for more than one year. On average, these entries out-yielded Calhikari-201 as much as 5%, have better stem rot resistance, and comparable milling yields. Experimental lines 04-Y-177 and 05-Y-196 are being purified in headrows and evaluated for milling and cooking qualities. Forty-four advanced lines were in preliminary yield tests and will undergo further grain quality evaluations and cooking tests.

Breeding for premium-quality medium grains seeks to improve upon the excellent grain and cooking characteristics of M-401, the late-maturing variety released in 1981. In 1999, later-maturing M-402, with more translucent grains and higher milling yields, was released. These varieties are being crossed with some proprietary medium grains to combine grain quality and good agronomic performance.

In 2007, 16 entries were in statewide yield tests. Eight of these entries have been in yield tests for more than one year. Compared to M-402, entry 04-Y-625 showed a 5% yield advantage in 2007. However, milling yields and blanking still need to be addressed.

Sixty-eight premium medium-grain lines were in preliminary yield tests. Eleven lines were selected based on higher average yields compared to check varieties, milling yields, and overall agronomic performance.

Specialty short grain rice accounts for about 20% of this project. These include waxy short grains, low-amylose short grains, and the bold grains. Quality evaluation and selection are difficult because grain- and cooking-quality attributes are poorly defined. Calmochi-101, a waxy short grain, was released in 1985. It has high yield potential, excellent blanking tolerance, and large kernels but has rough hulls. Calamylow-201, released in 2006, is the first and only low-amylose variety for California. Breeding for low-amylose and bold grain types will continue, with improved milling yields and agronomic performance being major objectives. In 2007, 11 waxy short grains, seven bold grains, and five low-amylose short grains were in statewide or preliminary yield tests.

Breeding for water weevil resistance has been temporarily discontinued because of difficulties in selecting for this attribute, such as erratic infestations and the lack of screening methods under controlled environments. Breeding for stem rot resistance remains an important component of the short grains project. Breeding for blast resistance will continue but receive less attention in coming years.

Rice pathology

Breeding for disease resistance is a cooperative effort between plant breeders and the RES plant pathologist. In 2007, about 2,500 rows were screened in statewide and preliminary yield tests for stem-rot and sheath-spot resistance. In the RES greenhouse, 450 entries were screened for resistance to sheath spot, 400 entries for Bakanae disease, and 5,000-10,000 entries for blast.

A rapid backcross program involving more than 660 crosses screened 2,800 seedlings for resistance to blast, and 24,000 seedlings each for stem rot and sheath spot resistance. An additional 6,200 rows of early generation material derived from crosses with resistant parents were also cycled through the disease nursery.

False smut, a disease new to California, was found by UC farm advisor Chris Greer in 2006 and should be watched closely in California, as this disease has been a problem in the southern United States.

Screening for stem-rot resistance usually begins with third-generation crosses. In 2007, there were 6,200 rows in the stem rot nursery, 3,955 of them drill seeded. Drill seeding creates a more uniform stand and better opportunities to screen for lodging.

Promising long-grain and short-grain resistant lines are emerging, but progress has been slow with medium grains. Several current varieties and stem rot resistant lines were evaluated for yield in an inoculated disease nursery. Over the last three years, the long-grain line 03-Y-496 continues to yield more than L-205 by nearly 17 percent. It has performed well in off-station trials as well. Medium grain entries yielded well but did not have desired levels of resistance.

Two long-grain and two medium-grain lines with resistance from O. rufipogon and two lines with resistance derived from Oryza nivara have been backcrossed with M-206. One hundred crosses were made in 2007 from these lines. Additionally, the mode of inheritance for O. nivara was studied in 3,500 transplants in 2007. Backcrossing will continue until progeny are ready for yield testing.

A greenhouse-screening program for experimental entries with sheath spot resistance not derived from wild species like O. rufipogon continues. This is especially important for medium grains, which do not have O. rufipogon-derived resistance. This testing revealed large differences in susceptibility to sheath spot. Sixty-six backcrosses were made in a bolstered effort to transfer sheath blight resistance from Teqing, Jasmine 85, and MCR10277 to M-206 and L-205.

Rice blast severity has been low in most years since it was first discovered in 1996. Most affected fields are on the west side of the valley. M-104 appears to be more susceptible than other varieties, followed by M-205. The first blast-resistant variety, M-207, was released in 2005 and was followed by M-208 in 2006. About 7,500 lines were screened for blast resistance in the greenhouse during 2007.

New breeding lines from the Philippines are being backcrossed into M-206 to incorporate broader blast resistance into this variety. Only genes with a wide spectrum of blast resistance are chosen. In 2007, 501 crosses were made. “Pyramided” genes would slow or eliminate the breakdown of major gene resistance.

Screening for Bakanae resistance continues in the RES greenhouse. Seed treatment research has been concluded. Backup chemicals have been identified should bleach no longer be available.


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