Rice Breeding Program - 2008




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Project Leader and Principal  Investigators

Kent S. McKenzie, Director

Farman Jodari, plant breeder, long 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 13 public varieties and basic seed of two Japanese premium-quality varieties were grown on 170 acres at the Rice Experiment Station (RES) in 2008.

The rice breeding program consists of four ongoing research projects developing California-adapted varieties for specific grain and market types. Farman Jodari continues his work on long grain rice. Virgilio Andaya is the project leader for premium quality, waxy, and California short grains and leads DNA marker research. Jacob Lage has assumed leadership for the Calrose medium grains with the retirement of plant breeder Carl Johnson after his many years of service at RES. Jeff Oster supports the breeding program’s efforts to improve disease resistance. Progress highlights from 2008 are reported below.

Breeding nurseries

Seeding of the 2008 breeding nursery began April 25 and was completed by May 21. A dry, cool spring and moderate summer temperatures characterized the 2008 growing season. Statewide average yields on the 517,000 harvested acres in 2008 were 8,320 pounds/acre, according to USDA statistics.

A total of 1,822 new crosses were made for rice improvement, bringing the total to 36,630 since 1969. Crosses made in early spring 2008 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 2008 RES breeding nursery occupied approximately 80 acres.  Water-seeded yield tests included 3,675 small plots and 3,245 large plots.  Small seed-increase plots and cooking samples were grown on 2.5 acres. 

The nursery included 56,065 water-seeded and 13,820 drill-seeded progeny rows. An estimated 200,000 panicles were selected from various second-generation populations for screening and advancement. Approximately 1,200 headrows of M-401, M-402, and Calamylow-201 were grown for breeder seed production.

The 2007-8 Hawaii winter nursery included 8,460 progeny rows and 583 first-generation crosses. The 2008-9 winter nursery, also with 8,460 rows, was planted November 5 and 6.  First-generation plants from 584 crosses were transplanted to the nursery between December 8 and 9. Selection and harvest was scheduled for April 2009, with seed to be planted at RES by late spring.

The 2008 cold-tolerance nursery at UC Davis contained 8,040 drill-seeded progeny rows for observation.  The San Joaquin cold tolerance nursery was planted in cooperation with two local growers.  This seven-acre, drill-seeded nursery included 18,000 rows, five acres of second-generation populations, and two small, drill-seeded yield tests.

Statewide yield tests

Statewide yield tests were conducted in grower fields and at RES in 2008 to evaluate promising advanced selections from all three maturity groups – very early, early, or intermediate-to-late. 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 688 entries and check varieties.  Superior entries advanced to 2009 statewide yield tests.

Calrose medium grains

Calrose medium-grain breeding focuses on high yield potential, improved milling yields, resistance to lodging and disease, seedling vigor, and resistance to cold-temperature blanking. 

Five Calrose medium-grain rice varieties are currently in production – M-104, M-202, M-205, M-206, and M-208:

·   M-104 is the only very early-maturing medium grain variety and is the dominant variety in the Delta region.

·   M-202 and M-206 are both early-maturing varieties with broad adaptation throughout rice country. M-206 continues to out-yield M-202 and also shows superior milling yield.

·   M-205 is the longest-maturing Calrose medium grain and by far the variety with the best resist­ance to lodging. Well-suited to warmer, more northerly locations, it is also characterized by excellent milling quality.

·   M-208 is the newest Calrose medium grain, a blast-resistant variety that is a good choice for those areas with a history of the disease.

A very-early experimental line, 05-Y-471, is under consideration for release as a new variety. It performs similar to or better than M-104. Its main improvement is better milling quality, especially at harvest moistures below 17 percent. This line would be targeted at the more productive areas of the Sacramento Valley rather than the Delta region. A well-adapted, very early variety would provide a new option to diversify rice crops with different maturities.

Several advanced experimental lines, including “Chinese Introgressions,” were tested in preliminary yield trials in 2008.  Although yielding less than M-206, these new lines outperformed other experimental lines (9,620 pounds/acre, compared to 9,310 pounds/acre). Results are encouraging and further crosses are under way.

Improved milling yield is one of the top two objectives in the Calrose medium grain project. M-206 is the standard for selection. Improved milling yield at lower moisture content could save on drying costs and also benefit the environment.

Progress is also being made on other objectives. A vigorous backcrossing project is under way to improve resistance to lodging and stem rot. Selection for blast-resistant material has been made more cost-effective and efficient with molecular markers. Research on the tall M-206 mutant for desirable traits is continuing. The upgrading of old greenhouses at RES should also open up new possibilities in the Calrose medium-grain program, especially for cold-tolerance screening.

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 the top priority, followed by resistance to cold-induced blanking and other agronomic and disease-resistance traits.

Conventional long grain L-206, released in 2006, has improved cooking quality, higher grain yield, and earlier maturity but slightly lower milling yield than L-204. Recent studies show, however, that L-206 is significantly more resistant to grain fissuring, an attribute that should provide more stable milling yield.

L-206 is a very early to early-maturing semidwarf that is well suited for all but the coolest rice-growing areas. 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 nine 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 9,210 pounds/acre at the cooler Sutter site and 10,280 pounds/acre at RES. The seven-year head rice yield averaged 62 percent.

Other promising conventional long grains being evaluated include 06-Y-513 and 06-Y-575.  The first, 06-Y-513, showed high yield potential in cooler-than-normal seasons during 2007 and 2008. Compared to L-206, 06-Y-513 showed a 3 percent higher milling yield and a similar or stronger starch profile. Entry 06-Y-575 is a high-amylose type, similar to L-205, with high yield potential, good milling, and blanking resistance. Both experimental lines were tested in the very early and early groups of statewide tests in 2008.

DNA markers were successfully used in 2008 to determine amylose synthesis genes in 1,300 long-grain breeding lines. Use of this technology is reducing the need for starch-profile characterizations.

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

Calmati-202, a true basmati released in 2006, is susceptible to cold-induced blanking and is therefore not recommended for cold locations. Yield potential is lower than L-205 and M-202. Grain and cooking quality is superior to Calmati-201. It 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 percent.

A new series of basmati selections with improved cooking quality advanced in statewide trials in 2008. Entries 07-Y-154 and 08-Y-138 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.

Efforts also continued in 2008 to improve jasmine types through pedigree and mutation breeding. Forty-eight advanced jasmine selections were tested.

Milling quality is another area of long grain improvement. Grain characteristics are being selected that will lend milling-yield stability to long-grain lines under adverse weather conditions.  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. Additional information about this project is available online at http://www.uark.edu/ua/ricecap/.

Stem-rot resistance from the wild species Oryza rufipogon has been transferred to a number of high-yielding, long-grain lines. Thirty-two entries with a range of stem-rot resistance were tested in 2008 statewide yield tests. A few entries showed low stem-rot scores, low blanking, and high milling yield.

Short grains & premium quality

The short-grain and premium-quality rice-breeding 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. Priority is on premium-quality short grains and medium grains because of their relative importance in the rice market. Development of DNA molecular-marker technology at RES is growing at a rapid pace. Markers that were developed for grain quality and blast resistance are now routinely used in all breeding projects.

S-102 is the dominant commercial variety 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 primary goal for conventional short grains is to develop a variety with improved yields, stem-rot resistance, smooth hulls and better cooking quality. In 2008, 36 lines were tested in preliminary yield tests at RES and may be advanced to statewide yield tests.

Premium quality is a term used to identify California medium grains like M-401 and the Japanese varieties Koshihikari and Akitakomachi. Calhikari-201, derived from a cross between Koshihikari and S-101, was the first premium short-grain public variety. Released in 1999, it is high yielding, early maturing, of good seedling vigor, and is lodging resistant. However, its grain quality does not equal Koshihikari, making it less acceptable to the Japanese market.

In 2008, 13 premium-quality short grains were in statewide yield tests. The grain yield of Calhikari-201 was variable, with an average of 9,400 pounds/acre in the very-early group to 8,000 pounds/acre in the early group. Entries in the early group that show a significant yield advantage will be advanced, pending evaluation for blanking, milling and cooking.

Experimental line 04-Y-177 showed comparable or better eating quality than Calhikari-201. It also averaged a 3 percent yield advantage and will be evaluated again in 2009. Altogether, 39 premium-quality short grain lines were evaluated in preliminary yield 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.

In 2008, 12 entries were in statewide yield tests. Sixty-four 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. Grain yields averaged between 7,900 pounds/acre to 8,500 pounds/acre, but cooking evaluations were excellent. Rigorous grain-quality evaluation and cooking tests were planned before advancing to statewide yield tests.

Specialty short grains include Calmochi-101, a waxy short grain released in 1985 and Calamylow-201, the only low-amylose variety for California.  Quality evaluation and selection are difficult because grain and cooking quality attributes are poorly defined. Breeding bold-grain types will continue but to a lesser extent. In 2008, 21 waxy short grains, two bold grains, and two low-amylose short grains were in statewide or preliminary yield tests.

New equipment in the DNA marker laboratory significantly increased the amount of rice materials tested. At least 80 percent of the activities are directed toward medium-grain breeding. About 4,000 early generation lines were screened for blast resistance. Another 2,000 plants were processed in backcrossing work with the plant pathologist.

An average of 1,500 lines were evaluated for a waxy gene marker in the long-grains program. Work on stem rot resistance is a top priority, as is the identification of markers for improved cooking quality, cold tolerance and other important traits.

Rice pathology

Breeding for disease resistance is a cooperative effort between plant breeders and the RES plant pathologist.  In 2008, about 2,500 rows were screened in statewide and preliminary yield tests for stem-rot and sheath-spot resistance.  In the greenhouse, 450 entries were screened for resistance to sheath spot and 450 entries for Bakanae disease.

A rapid backcross program involves screening about 1,300 entries for blast, and 62,000 plants for stem rot and 41,000 for sheath spot resistance. An additional 4,000 rows of early-generation material, derived from crosses with resistant parents, were also cycled through the disease nursery.

Screening for stem-rot resistance usually begins with third-generation crosses. In 2008, there were 6,800 rows in the stem rot nursery, 5,300 of them drill seeded. Promising long-grain and short-grain resistant lines are emerging, but progress has been slow with medium grains.

Because progress with medium grains has been slow, an immediate backcross program was initiated. Two long-grain and two medium-grain lines with resistance from O. rufipogon and two lines with resistance from O. nivara have been backcrossed with M-206. Fifty-four crosses were made, since stem rot resistance from O. rufipogon is derived from more than one gene. Also, the mode of inheritance of resistance in O. nivara was studied in 3,500 transplants last year.

Greater emphasis will be placed on rapidly advancing generations from earlier backcrosses. It may be possible to combine resistance from O. rufipogon and O. nivara after this backcrossing scheme is completed.

Fifty resistant and 50 susceptible lines identified over the years in the program to transfer resistance from O. rufipogon were grown as transplants this year. About 1,000 first-generation backcrossed transplants derived from M-206 and 87-Y-550 were field evaluated for stem rot resistance. The best and worst of these plants will be used to develop molecular markers to assist in genetic mapping.

A greenhouse screening program has been set up to test statewide yield entries for sheath-spot resistance. This is especially important for the medium grains, which do not yet benefit from resistance derived from O. rufipogon. Sheath spot is more widespread than stem rot, and can cause significant damage. In addition, an immediate backcross program was begun to transfer sheath spot resistance from Teqing, Jasmine 85, and MCR10277 to
M-206 and L-205. A total of 117 crosses were made in this effort in 2008. Rice CAP researchers have found one molecular marker associated with about 29 percent of the resistance found in Jasmine 85, an encouraging development.

Work on blast continues but is not the top priority it was several years ago. Severity of the disease, which first appeared in California in 1996, has been much lower in recent years. Most fields affected by it are located on the west side of the Sacramento Valley. M-104 appears most susceptible, followed by M-205. The first blast-resistant variety, M-207, was released in 2005, followed by M-208 in 2006.

New lines with broader resistance to different races of blast have been brought through quarantine from the International Rice Research Institute in the Philippines. A backcross program started in 2005 is attempting to introduce these genes into M-206. Seven backcrosses were made and screened for blast resistance. These lines will be evaluated for agronomic traits. Backcrossing continues to transfer other genes into M-206 with the aid of molecular markers (295 crosses in 2008). This project will be completed for all genes by 2010.


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