Rice Breeding Program, 2017


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

Paul Sanchez,

plant pathologist

Cynthia Andaya, research scientist, DNA marker laboratory

The California public rice breeding program has developed 47 improved rice varieties since accelerated research began in 1969. Foundation seed of 17 public varieties and basic seed of one Japanese premium quality variety were produced on 134 acres at the Rice Experiment Station (RES) in 2017.

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 oversaw premium quality and short grains breeding. Farman Jodari led the long grain project and also served as liaison with Southern U.S. breeding programs. He had been working at RES since 1999 but retired in June 2017. Paul Sanchez led the rice pathology laboratory in 2017. The plant pathologist supports efforts to improve disease resistance in all projects. Cynthia Andaya is in charge of the DNA marker laboratory and the grain quality lab. Director Kent McKenzie oversees administration of the Rice Experiment Station. Progress highlights from 2017 are reported below.

Breeding nurseries

Seeding of the 2017 breeding nursery was delayed because of a heavy winter and extended spring rains. Drill seeding of the second-generation maintenance nursery, two preliminary yield plots, and milling plots occurred between May 8 and May 16. Water seeding began May 22 and was completed May 31.

A total of 1,124 crosses were made for rice improvement, bringing the total to 49,043 since 1969. Crosses made in early spring 2017 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 breeding nursery occupied about 75 acres. Water-seeded yield tests comprised 2,832 small plots and 2,468 large plots. The nursery included 51,500 water-seeded pedigree rows, 1,485 drilled second-generation plots, and 20,460 drill-seeded seed maintenance rows. A total of 1,408 rows were planted for seven advanced lines selected for preliminary headrow increase—in addition to 1,819 rows of herbicide resistant materials. An estimated 150,000 panicles were selected from various second-generation populations for screening and advancement.

Foundation seed headrows were grown for breeder seed of L-206, L-207, M-209, M-105, Calhikari-201, and Calhikari-202. Headrows of experimental lines 15Y84 and 12Y3097—both proposed for release as new varieties in 2018—also were grown. Headrow seed can be used for several years to produce breeder seed because it is stored under low temperature and proper humidity conditions.

The 2017–2018 Hawaii winter nursery was comprised of 7,280 progeny rows, 880 headrows of 17Y3000, and 580 transplanted rows of first-generation and miscellaneous materials. The rows were dry seeded between October 31 and November 2, 2017. First-generation seedlings were transplanted November 20, 2017. Selection and harvest was set for April 2018, 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 a local grower. This three-acre, drill-seeded nursery included 3,600 rows, and 455 six row, second-generation plots. Weed control was good, although damage from geese caused poor stand establishment for about one-third of the population. Minimal cold-induced blanking was observed in the rows and the second-generation populations.

Statewide yield tests

Statewide yield tests were conducted in grower fields and at the RES in 2017 to evaluate promising advanced selections from all three maturity groups—very early, early, or intermediate/late. More detail is reported in the Rice Variety Trials section of this annual report and online at rice.ucanr.edu

Preliminary yield tests are the initial step of replicated large-plot testing for experimental lines. These tests included experimental entries, as well as check varieties. Yield of the top experimental lines compared well with check varieties. Superior entries will be advanced to 2018 statewide yield tests.

Variety Grain Yield
Days to
Plant Height
M-209 10,330 1.9 79 102 17
M-205 10,220 4.8 81 101 8
M-206 10,000 4.9 71 102 61
M-208 9,760 4.8 71 103 48
M-105 9,500 4.9 69 100 56
M-104 9,230 4.8 66 98 40

Calrose medium grains

The predominant rice varieties planted in California are medium grains, commercially and internationally known as Calrose rice. More than 80% of California rice acreage is planted to medium grains. Breeding for medium grain rice comprises about half the rice breeding program. A third of this project is devoted to premium quality medium grain varieties that previously had been assigned to the short grains project.

The main goal of the medium grains breeding project is to develop new rice varieties with high, stable grain and milling yields without sacrificing the excellent grain quality of the Calrose varieties. To achieve stable grain yield across the region, emphasis is given to selecting materials with high seedling vigor and tolerance to low temperature-induced blanking. Milling yield in terms of both total and head rice are given top priority. Breeding materials are planted mostly by hand at the RES breeding nursery in May, while the second-generation nursery and seed maintenance plots are drill planted in the last week of April. Seed increase and generation advance also takes place at the Hawaii Winter Nursery.


Calrose varieties that are still in commercial production in California are used as checks in preliminary and advanced yield tests. In 2017, these included M-105, M-205, M-206, M-208, M-209, and M-104. The latter will be replaced with M-105 as a very early check, while M-208 will be phased out as the blast resistant check. M-209 has been the top-yielding check variety for several years, with an average grain yield of 10,330 pounds/acre in 2017. The two-week delay in planting the breeding nursery in 2017 probably affected the yields of early maturing varieties M-105 and M-104, as well as M-206.


Premium quality medium grain entry 12Y2175 produced outstanding yields in 2017. It was the top yielder at RES, with grain yield ranging from 11,500 pounds/acre to 11,800 pounds/acre—about 18% to 22% over M-206. This advanced line heads about 10 days later than M-206 and two days later than M-209. Further evaluation of cooking characteristics and grain quality through internal and external evaluations will determine whether 12Y2175 is of M-401 premium quality.

ADVANCED LINE 12Y3097: M-210

Advanced line 12Y3097 is being recommended for release in 2018 as a blast resistant, high yielding, early maturing, glabrous Calrose medium grain. It was in foundation seed increase in 2017 and has a proposed name of M-210.

12Y3097 is one of the M-206 blast resistant isolines containing individual blast resistant genes developed with marker-aided backcrossing and selection. This line is a replacement for M-208, which contained the Pi-z gene found to be ineffective against the new IB-1 blast strain. The line performed similarly to M-206 in grain yield, milling characteristics, and other agronomic traits.

The overall grain yield of 12Y3097 across 43 statewide experiments conducted between 2013 and 2017 averaged 9,300 pounds/acre, compared to 9,370 pounds/acre for M-206 and 8,910 pounds/acre for M-208. Compared to M-208, 12Y3097 reached 50% heading in 83 days, had slightly shorter plant height, and similar seedling vigor and lodging. It may not be suitable for colder areas.

Milled rice grains of 12Y3097 were heavier and slightly wider than M-208 and M-206. Grain length is between M-206 and M-208. With these grain characteristics, it can be comingled with other Calrose varieties. Milling data showed that the head rice yield of 12Y3097 when harvested at 19% to 22% grain moisture averaged 65/70 (head/total), compared to 64/69 for M-206 and 63/68 for M-208. When cut at moistures above 22%, milling yield of 12Y3097 improved to 66/70. Head rice decreased on all entries cut below 19% harvest moisture.

Average apparent amylose (starch) content and protein content of 12Y3097 is 15.7% and 6.6%, respectively. Those values are very close to M-206 and M-208. All three have low gel type typical of Calrose medium grains. Cooking characteristics are similar to M-206. Cooking quality evaluations have been favorable.

Screening for blanking showed that 12Y3097 had better cold tolerance than M-208 and similar cold tolerance to M-206. In addition to being blast resistant, 12Y3097 reacted comparably to check varieties against aggregate sheath spot. Reaction to stem rot was slightly better than M-206 and M-208.

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.

Entries evaluated in various yield tests in 2017 included 390 conventional long grains, 108 basmati types, 65 jasmine types, and seven aromatic long grains. Twenty-seven were in statewide tests.


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 on milling yield and cold tolerance.

L-206, L-207, and A-202 were the long grain check varieties in 2017 statewide tests. L-206 has been the standard check since its release in 2006. It is an early maturing, high yielding, conventional long grain with good cooking quality.

L-207, released in 2016, is the newest conventional long grain. It is a high yielding, intermediate height, and early maturing variety with Southern long grain cooking quality. It is adapted to most areas except the San Joaquin region. Its head rice yields range between 63% to 67%, compared to 62% to 63% for L-206. However, L-207 has lower stem rot and aggregate sheath spot resistance than L-206.

Variety Grain Yield
Days to
Plant Height
L-207 10,710 409 74 109 12
L-206 10,280 408 71 94 18
A-202 9,440 409 73 102 15

A-202 is a conventional aromatic variety released in 2014 as a replacement for A-301. A-202 is nine days earlier, taller, with higher seedling vigor and comparable flavor characteristics. Milled kernels of A-202 are slightly bolder than A-301 with starch characteristics typical of conventional long grains. A-202 is adapted to Butte, Colusa, Yuba, Glenn, and Sutter counties but not colder rice growing areas.

An advanced conventional long grain line, 14Y1006, performed well in 2017 statewide tests. Grain yield of 14Y1006 at RES reached 11,360 pounds/acre, compared to 10,707 pounds/acre for L-207 and 10,280 pounds/acre for L-206. Pooled grain data from all statewide test locations (except Yolo County) show a significantly higher yield advantage over L-206. Milling yield data shows 14Y1006 is similar to L-207 and less chalky. Compared to L-206, it headed in 69 days (two days earlier) and is taller with higher lodging. Cooked grain texture is similar, with subjective scores favoring 14Y1006. Headrow production of this line is planned for 2018.


A jasmine-type long grain line, 15Y84, has been recommended for release in 2018 as “Calaroma-201.” It is a high yielding, semidwarf, early maturing, glabrous, aromatic developed as an alternative to imported Thai jasmine.

Over a three-year period,15Y84 compared closely with L-206 and A-202. In 2017 it was entered in all locations of the statewide yield tests. The overall grain yield of 15Y84 averaged 9,450 pounds/acre, compared to 9,310 pounds/acre for L-206 and 8,890 pounds/acre for A-202.

It reached 50% heading five days later than L-206 and one day later than A-202. 15Y84 is slightly taller than L-206 but shorter than A-202. It demonstrated comparable seedling vigor and lodging scores. Area of adaptation is similar to L-206, but it is not recommended for colder rice growing areas.

Grains of 15Y84 are lighter, longer, and narrower than L-206 and A-202. The head rice yield of 15Y84 harvested between 19% and 21% moisture was 60/67 (head/total), compared to 61/70 for L-206 and 61/68 for A-202.

Apparent amylose, protein percentage, and gel type of 15Y84, L-206, and A-202 were taken and independently evaluated. Amylose content of 15Y84 is 15.76%, compared to 22.41% for L-206 and 22.38% for A-202. Having a low amylose content and low gel type, 15Y84 cooked softer and stickier than the conventional long grains in this comparison. Feedback on eating quality from Asian consumers of imported jasmine rice also was favorable, indicating that 15Y84 can be an excellent alternative to imported Thai jasmine.

Because of the general sensitivity of long grains to cold temperatures, 15Y84 is recommended only for warmer areas or those areas where L-206 and A-202 perform well. Reaction to stem rot is between L-206 and A-202, with L-206 being more susceptible. However, 15Y84 is more susceptible to aggregate sheath spot. Its susceptibility to blast is similar to L-206 and A-202.

Short grains

The short grain project includes conventional short grains and specialty types such as waxy rice, low amylose short grains, waxy short grains, Arborio types, and premiums. New lines are bred and selected for improved, stable grain yield and yield related traits, milling and cooking quality, blanking resistance, lodging resistance, very early to early (and uniform) maturity, short flowering duration, and resistance to diseases.

The project is approximately 30% conventional short grains, 35% waxy, 20% premium short grains, 10% Arborio, and 5% low amylose. The short grain entries evaluated in 2017 yield tests included 118 conventional short grains, 69 premium short grains, 147 waxy short grains, 17 low amylose, and 47 Arborio types. Twenty entries were entered in statewide yield tests.


Experimental lines in nurseries and yield tests were compared against check varieties, including S-102, Calhikari-201 (CH-201), Calhikari-202 (CH-202), Calmochi-101 (CM-101), Calmochi-203 (CM-203), Calamylow-201 (CA-201), and the Arborio-type germplasm line 89Y235. Some background on these varieties includes:

  • S-102, released in 1996, is the standard short grain check. It is very early maturing, with large seeds, pubescent, and has good cold tolerance.
  • CH-202, released in 2012, is the latest premium quality variety. It is early, short, pubescent, yields higher than CH-201, has better eating quality, smaller grains, and higher milling yields.
  • CM-203, released in 2015, is the latest waxy or sweet rice. It is a high yielding, glabrous, early maturing variety released as an alternative to CM-101.
  • CA-201 is no longer in seed production but will serve as a check for low amylose lines.
  • 89Y235 is a germplasm with big seeds.

In 2017 statewide yield tests at RES, grain yield of CM-203 was the highest at 10,580 pounds/acre, followed by S-102 at 10,060 pounds/acre. The yield of CA-201 was the lowest at 5,990 pounds/acre. Seedling vigor of CH-201 was still the best among the short grains. However, the premium short grains still lagged behind in terms of straw strength. Number of days to heading among check varieties ranged from 72 to 76 days.


A conventional short grain line, 10Y2043, continued to show yield superiority over S-102 in almost all statewide yield tests in 2017. Grain yield of 10Y2043 averaged across eight locations in 2016 was 11,330 pounds/acre (an 18% yield advantage over S-102). Similarly, in 2017 its grain yield at RES was 11,220 pounds/acre. Pooled average grain yield advantage from 2015 to 2017 ranged from 16% to 23% in all locations except San Joaquin, where it was 2% lower than S-102.

Herbicide resistant rice

A three-year research project on herbicide tolerant rice concluded in 2016. This project produced a non-GMO rice trait providing resistance to the herbicide oxyfluorfen, marketed as Goal® 2XL and Goal Tender®.

This trait was discovered in a population of M-206, currently the most widely grown Calrose variety in California. Genetic studies by RES scientists showed that this trait is inherited by a single recessive gene. If has been designated as ROXY™-- an acronym for resistance to oxyflourfen.

Transfer, selection, and recovery of the ROXY™ trait to other varieties and grain types has be accomplished by the breeding program. Field and greenhouse research on rice weed control from 2015 to 2017 was conducted at RES and at nine off-station locations.

Results of these experiments show that oxyflourfen applied preplant in a water-seeded system provides high levels of rice weed control with acceptable levels of crop safety. Tests in 2017 also show very high levels of weed control in combination with other registered herbicides. Furthermore, it was effective in drill-seeded rice with a preplant and/or preflood application.

The use of oxyfluorfen with an adapted rice variety containing the ROXY™ trait could offer a number of advantages, including:

  • Application could be made on dry fields in the final steps of seed bed preparation
  • Use in proximity to sensitive areas or crops could be possible
  • Resistance to contact herbicides has not been reported for California rice weeds
  • As an off-patent herbicide, oxyfluorfen could result in significant cost savings to rice growers

A patent for this technology has been filed. The effort is supported by the California Rice Commission, California Rice Research Board, and California weed scientists. Research on breeding, genetics, efficacy, and data requirements to register oxyfluorfen for application on California rice is underway.

Seedling vigor is similar, but 10Y2043 heads about two to four days later and has a greater tendency to lodge. Grains of 10Y2043 are smaller than S-102, have a similar length/width ratio, and are less chalky. It has a glabrous or smooth hull compared to the pubescent grains of S-102. Foundation seed of 10Y2043 will be produced in 2018.


Premiums—Much effort goes into evaluating advanced lines for grain and cooking quality. Screening is difficult, so equipment upgrades such as better rice cookers and taste and grain analyzers are important.

In 2016, early Koshihikari mutants were purified and confirmed with DNA analyses. The cooking quality of these early lines is under evaluation.

Waxy—Calmochi-203 was released in 2015 to give growers an alternative to Calmochi-101 (released in 1985). CM-101 had been the standard of quality for the sweet rice market in California. However, its yield potential was significantly below CM-203. Despite its dramatic yield advantage, CM-203 has not been accepted in the market because of grain quality differences. Breeding efforts are underway to further improve the quality of sweet rice and couple that with higher yield potential.

Low amylose and Arborio types—The status of the California market for low amylose short grains, as well as demand for Arborio types, has not been determined. Nonetheless, breeding efforts continue on a limited scale for both types. In 1994, RES released 87Y235 as an Arborio-type germplasm source. It is grown commercially in small acreage. Although seed production of CA-201 has been discontinued, there is some small commercial production of this specialty type.

DNA marker laboratory

The DNA marker laboratory supports the different breeding programs and special projects. The lab is involved in marker-aided selection for blast resistance, grain quality, aroma, and herbicide resistance; DNA fingerprinting and purity testing of advanced lines; genetic mapping of stem rot resistance genes; and the development of mutant populations for herbicide resistance.


Marker-aided selection for both blast resistance and grain quality is now a routine part of work in the DNA marker laboratory. In 2017, a total 7,594 breeding lines were screened for blast resistance; 3,080 lines for grain quality and aroma; 6,248 lines for herbicide resistance; and 343 lines for stem rot resistance. A total of 17,265 lines were screened for four targeted traits, generating 30,607 relevant data points.

Marker-aided selection for blast resistance and grain quality averaged 9,740 lines per year between 2011 and 2017. In 2013 alone, the lab analyzed 16,700 lines for those two traits. Based on the seven-year record, current equipment, and staffing, the lab is capable of handling approximately 17,000 rice materials annually.


Another important function of the DNA lab is to assist in variety identity and purity assessment—DNA fingerprinting. The lab has developed a panel of DNA markers that distinguish medium grain varieties from each other. This has already been helpful in confirming seed contamination in grower fields. Markers that can distinguish long grain and short grain varieties also have been identified.

Fingerprinting requests vary, depending on the needs of the breeding program. In 2017, the lab received 287 lines for fingerprinting to confirm new crosses, putative M-209 mutants, RES germplasm 89Y235, and various samples from foundation seed fields. Some growers also requested variety identification.

An annual average of 2,166 lines were fingerprinted from 2012 to 2017, generating a total of 24,022 useful data points using at least 10 markers for purity and uniformity testing. The greatest number of fingerprinting requests, 5,400 lines, occurred in 2016. On average, the DNA lab analyzed 12,800 lines a year, generating 63,500 data points. (This includes both marker-aided materials and DNA fingerprinting.) The greatest number of lines examined by the lab was 18,600 in 2012.


Several years ago, the Rice Experiment Station embarked on a project to find herbicide resistant rice using induced mutation. In 2014, a mutant resistant to the herbicide oxyfluorfen was isolated from an M-206 mutant population. To determine the genetic location of herbicide resistance, mapping populations were generated with a cross between A-202 and the M-206 mutant, 14G7. Initial mapping studies by the lab determined the chromosome location of the ROXY™ gene. A fine-mapping population from a cross of 14G7 and L-206 also was developed. A total of 1,116 lines were used for fine mapping from this population to further narrow the genetic region of interest and to reduce the number of candidate genes.

Rice pathology

p> Breeding for disease resistance is a cooperative effort between rice breeders and the RES plant pathologist. Upon the departure of Paul Sanchez in October 2017, DNA marker lab research scientist Cynthia Andaya temporarily added plant pathology to her responsibilities.

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 both stem rot and aggregate sheath spot resistance. In addition, early generation materials derived from breeder crosses have been cycled through the disease nursery to verify disease resistant lines.


A major effort on blast resistance was initiated in 2005 by Jeffrey Oster, who retired in 2015 after more than 30 years as the rice pathologist at RES. This effort involved backcrossing to introduce blast resistance genes from various blast resistant germplasm in the M-206 genetic background.

The first blast resistant variety, M-207, was released in 2005, followed by M-208 in 2006. However, symptoms of the blast disease were observed on M-208 in 2009. Further research determined the existence of a new, significantly different race of the fungus. The backcross work utilized genes with a wide spectrum of resistance. In 2012, four, near-isogenic lines of M-206 were entered into statewide tests. The blast resistant lines performed better than M-208 and were comparable to M-206. One of the near-isogenic lines with blast resistance, advanced line 12Y3097, has been recommended for release as a new variety, M-210, to replace M-208.


In 2017, screening for stem rot resistance included evaluations on 3,600 rows. A few crosses were made to combine stem rot and blast resistance. Generations were advanced with blast and stem rot screening occurring in alternate generations. Aggregate sheath spot screening was performed on purified lines.

Mapping populations previously had been scored for stem rot resistance. Also, 660 rows were scored in the field for fine-mapping of stem rot resistance from the wild species, Oryza rufipogon. Some materials identified as resistant in 2014 were again resistant in plots and rows, but many others were inconsistent. Lack of uniformity in the nursery may be at least partly at cause.

Variations in stem rot scoring in 2016 were observed among lines in the mapping population. In 2017, greenhouse evaluations were conducted to confirm the degree of susceptibility and resistance of selected lines.

A yield study on the effect of stem rot on varieties M-206, M-209, L-206, L-207, S-102, and S-301 was conducted in small plots at RES in 2017. Grain yield was 10,130 pounds/acre for M-206 and 10,170 pounds/acre for M-209. L-206 registered a yield of 9,710 pounds/acre, while L-207 yielded 10,730 pounds/acre. S-102 yield was 10,640 pounds/acre. L-207 was found to be more resistant to stem rot and consistently yielded high in fields inoculated with stem rot. M-206 was found to be moderately resistant in this study.


The backcross program also aims to transfer aggre-gate sheath spot resistance genes from Teqing, Jasmine 85, and MCR10277 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. These materials have been put in cold storage for future use.

Aggregate sheath spot screening in the greenhouse expanded to include preliminary trial entries, as well as statewide entries.


The building blocks for any breeding program are cultivars with traits desirable in commercial production. Two hundred lines from the Southern U.S. have been received for evaluation and use in the breeding program at the Rice Experiment Station. The seeds of each line were treated and germinated in the laboratory. These were grown to full maturity and screened inside the greenhouse. All plant introductions were grown and released for breeder use under procedures developed and approved by the U.S. Department of Agriculture and the California Department of Food and Agriculture to prevent introduction of exotic insect pests and diseases, as well as weedy red rice in California.