Rice Breeding Program, 2020

 

Kent McKenzie, Director, retired 12/31/2020

Virgilio Andaya, director of plant breeding; plant breeder, Clarose medium grains

Teresa De Leon, plant breeder, short grains

Shyamal Talukder, plant breeder, long grains

Cynthia Andaya, research scientist, DNA marker laboratory

The California public rice breeding program has developed 51 improved rice varieties in 11 different market types since accelerated research began in 1969. Foundation seed of 17 public varieties and one experimental line were produced at the Rice Experiment Station (RES) in 2020.

The rice breeding program’s primary research objective is the development of high-yielding, high-quality rice varieties that are commercially competitive in the world market. Other specific breeding objectives include grain quality and milling yield, cold tolerance and seedling vigor, early maturity and strong culm, and disease resistance.

Virgilio Andaya is director of plant breeding and is responsible for building the breeding and research team and for providing guidance to achieve goals for all grain types and market classes. He primarily breeds medium grains.

Teresa De Leon leads the short grain program and has temporarily taken charge of stem rot disease field screening and quarantine of introductions.

Shyamal Talukder leads the long grain program and serves as the liaison to breeding programs in the Southern U.S. and handles screening of the Uniform Rice Regional Nursery.

Cynthia Andaya is the research scientist in charge of the DNA marker laboratory (now the genetics lab). The lab supports all breeding projects with marker-assisted selection, purity and uniformity testing through DNA fingerprinting, development of mutant populations, and performing genetic studies for traits important to California.

Kent McKenzie retired from his position as RES director at the end of December 2020. He led the special project developing a non-GMO herbicide tolerant rice called ROXY®. He is continuing to serve as a consultant to the Rice Experiment Station and Albaugh LLC. A shared partnership and commercial agreement has been reached with Albaugh LLC and the California Cooperative Rice Research Foundation (CCRRF).

Breeding nurseries

The breeding nursery in 2020 was composed of 50% medium grains, 25%, short grains, and 25% long grains. Based on market class, about half is conventional rice and half is specialty types. A total 977 crosses were made in 2020, bringing the total to 52,416 since 1969.

Because of favorable conditions, RES planting was almost two weeks earlier than in 2019. Drill-seeding of second generation populations was done on April 22 and 23. Drill seeding of seed maintenance was done May 6 and 7. Water-seeding of progeny rows, preliminary yield tests, advanced yield tests and other breeding lines started on May 4 and was completed on May 13.

A total of 501 entries were evaluated in the advanced yield tests and 687 entries in the preliminary yield tests. Preliminary yield tests are the initial step of replicated large-plot testing for experimental lines and superior entries before being advanced to statewide yield tests.

The breeding nursery included 31,668 water-seeded pedigree rows, 548 drill-seeded second-generation plots, and 12,000 drill-seeded seed maintenance rows.

The Hawaii Winter Nursery shortens the product development timeline by at least two years through advancing materials in the off-season. In 2020, however, the nursery had to be planted without the presence of any RES employees because of the pandemic. Seeds and layout were sent about two weeks earlier than normal in an effort to catch more favorable conditions for rice growth and development. All planting was conducted by a local crew with supervision from RES through a live call.

The 2020-21 winter nursery consists of 4,440 regular rows and 578 transplanted rows. The second generation rows were dry-seeded October 13, while the first generation seeds were planted in pots on October 12. Seventy percent of seedlings were transplanted on November 10, with the remainder transplanted November 17. Harvested seeds are to be planted in the 2021 breeding nursery at RES.

The San Joaquin cold tolerance nursery was planted in cooperation with a local rice grower. The three-acre, drill-seeded nursery included 3,840 rows of advanced breeding materials, 423 second generation plots, and 29 third generation ROXY® plots.

Statewide yield tests

Statewide yield tests were conducted in grower fields and at the RES in 2020 to evaluate promising advanced selections from all three maturity groups—very early, early, or intermediate/late. More details can be found in the Rice Variety Trials section of this annual report.

Plant breeder Dr. Teresa DeLeon water seeding a 10x20' yield plot in the RES nursery

Calrose medium grains

The predominant rice varieties planted in California are medium grains, commercially and internationally known as Calrose rice, and account for more than 80% of California rice acreage. Breeding for medium grain rice, including premium quality, comprises about half the rice breeding program.

The main goal of the medium grains breeding project is to develop new rice varieties with high, stable grain and milling yields with excellent eating and cooking qualities. Huge emphasis is given to selecting materials with high seedling vigor, improved cold tolerance, and excellent grain quality attributes sought by the rice market. Resistance to stem rot and rice blast diseases is another breeding focus. Development of medium grain varieties with oxyfluorfen herbicide resistance is now an integral part of the medium grains breeding project.

M-211 release

In early 2020, the experimental line 12Y2175 was approved for release as M-211. It is a high-yielding, semi-dwarf, early maturing, glabrous, high-quality medium grain. It has excellent yield potential, outstanding grain characteristics, and cooking quality superior to current Calrose varieties. M-211 is the first to be classified as a premium Calrose.

Its area of adaptation is similar to M-205 and M-209—the warmer regions of the Sacramento Valley. M-211 is susceptible to blast. Agronomic and yield performance in 2020 statewide testing showed M-211 superior to check varieties M-209 and M-206. M-211 out-yielded M-206 by 14% at RES in 2020 and registered an overall yield advantage of 12% to 15% in four to six years of testing. M-211 out-yielded M-209 at RES by 1% to 3% in 2020, with a 5% to 9% overall average across years. Grain yield did best under high-yielding, favorable environments such as those in Butte County but poorly in colder rice growing areas such as south Yolo County.

Milling attributes, particularly total and head rice percentage across harvest moistures, are an especially important consideration in releasing a new medium grain. Although its cooking and taste qualities are outstanding, M-211 milling characteristics are not at as good as M-206 but far better than M-401. M-211 is more sensitive to harvest moistures below 20%. Therefore, it is essential that M-211 be harvested at high moistures like any other premium rice.

M-211 consistently received high marks from mills and marketing organizations for its cooking quality and overall acceptability to the rice market.

Check variety performance

Check varieties used in statewide testing include M-105, M-206, M-209, M-210, and M-211.

M-206 and M-210 averaged 9,050 pounds/acre and 9,080 pounds/acre, respectively. M-210, the only blast resistant variety in commercial production, is a good alternative to M-206 in areas with that disease problem. M-209 yielded 9,380 pounds/acre, while M-211 yielded the highest among the medium grain checks with 9,600 pounds/acre.

In comparison of grain characteristics and milling performance of the medium grain checks, M-211 has the biggest and heaviest kernels but also has slightly more chalkiness in the milled grains. Head rice percentage of M-211 (61/72 head/total) is lower than M-206 (65/72 head/total) and M-105 (69/73 head/total). These results show that M-211 and M-209 should not be harvested at low moistures because of their tendency to break.

Promising advanced lines

The medium grain project tested a combined total of 885 entries in 2020—599 preliminary lines, 159 advanced lines, 59 advanced ROXY® lines, and 68 statewide entries. These advanced materials were composed of regular and premium medium grains, blast and stem rot resistant lines, specialty type fragrant medium grains, the herbicide resistant ROXY® lines, and lines with combinations of traits such as herbicide and blast resistance. All were evaluated against check varieties for milling and quality attributes, tolerance to cold and disease, and overall agronomic performance. Exceptional materials are further purified and evaluated for cooking and quality.

Several promising lines registered a grain yield advantage over check variety M-210 (9,080 pounds/acre) in two-rep preliminary and two-rep and four-rep advanced tests at RES, including 18Y3018 (9,370 pounds/acre) and 19Y3088 (9,670 pounds/acre). These two entries matured four days later than M-210, but with better lodging resistance. A stem rot resistant line, 19Y3035, registered 9,540 pounds/acre. All three selections may be entered in four-rep advanced statewide tests in 2021, pending further grain quality and cooking evaluation.

Variety Grain Yield
(lbs/acre)
Harvest
MC %
Seedling
Vigor
Days to
Heading
Plant
Height(cm)
Lodging
(percent)
M-105 9,170 17.3 4.83 84 96 38
M-206 9,050 18.3 4.80 85 98 33
M-209 9,380 18.3 4.83 91 99 24
M-210 9,080 17.9 4.82 85 99 27
M-211 9,600 18.2 4.82 91 101 25

ROXY® line recommended for foundation seed

The medium grains project began making crosses of an oxyfluorfen herbicide tolerant M-206 mutant in 2014. As of 2020, 514 crosses have been made with this ROXY® rice.

Sixteen herbicide tolerant medium grains were included in statewide tests in 2020. Two advanced lines, 17Y3000 and 19Y4000, underwent expedited selection in 2020. Compared to M-206 (9,050 pounds/acre), these lines registered 8,980 pounds/acre and 8,910 pounds/acre, respectively.

Agronomic attributes are described as remarkably similar. For grain attributes, 19Y4000 is better in terms of chalkiness and overall grain appearance. It has bigger and heavier grains compared to M-206, with similar, if not better, milling characteristics. Cooking evaluation also revealed better sensory scores for 19Y4000. It also is resistant to blast disease. 19Y4000 will be recommended for foundation seed production in 2021.

Other promising herbicide resistant lines yielded well in a separate herbicide test and will be entered into the statewide tests in 2021, pending grain quality evaluation.

Long grains

The long grains 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.

Yield and agronomic performance

Test materials in the 2020 statewide tests were compared to the long grain check varieties L-207, L-208, Calaroma-201, and A-202 for grain yield and agronomic performance. Milling characteristics, grain quality, blanking, and disease reaction also were analyzed.

L-207 is a conventional long grain with higher yields, intermediate height, early maturing date and desirable cooking quality similar to Southern long grains. It is adapted to most rice growing areas except San Joaquin County. L-208 is the newest conventional long grain with agronomic characteristics, adaptation, milling, and cooking quality similar to L-207.

Calaroma-201 is a jasmine type long grain with aroma similar to typical aromatic long grains, but taste characteristics close to Thai jasmine quality. It has an area of adaptation similar to L-207. With its low gel type, it cooks softer than other long grains.

A-202 is a conventional aromatic variety released in 2014 as a replacement for A-301. It heads nine days earlier than A-301, is taller, and has a significantly higher seedling vigor score. Milled kernels of A-202 are slightly bolder than A-301. Starch characteristics are typical of conventional long grains. It is not recommended for cooler areas.

Based on pooled averages from very early, early, and intermediate/late testing groups, L-208, L-207, and Calaroma-201 had higher yields at RES compared to other statewide locations. A-202 had higher yield in other statewide locations.

Yields for L-208 were 10,733 pounds/acre at RES, 10,553 statewide. For L-207, yields were 10,300 at RES, 10,216 pounds/acre statewide. For Calaroma-201, the figures are 9,943 pounds/acre at RES, 9,716 statewide. For A-202, yields were 8,893 pounds/acre at RES, 9,146 pounds/acre statewide.

The new variety, L-208, had about a 3% higher yield than L-207 in 2020. It performed better and had higher yield in eight out of 10 statewide experiments, the exceptions being in Yuba and Sutter counties. Average head rice yield was 63.3%, with a range of 57% to 66% at various harvest moistures, which was 2% higher than L-207.

Head rice yield of Calaroma-201 was 63.1%. For A-202, it was 60.1%.

None of the varieties had lodging at RES except very low lodging (5.4%) in L-208.

Promising long grains

Four experimental lines showed promise in the 2020 statewide yield trial—19Y1071, 19Y1008, 18Y1024, and 17Y1087.

Advanced line 19Y1071 is a jasmine type long grain in the statewide trial for the first time in 2020. It was planted in three locations and outperformed Calaroma-201 for yield by 4.8%. Average yield was 10,760 pounds/acre at RES and 9,870 pounds/acre statewide. Calaroma-201 yield was 9,943 pounds/acre at RES and 9,716 pounds/acre statewide.

Another newcomer, 19Y1008, is a regular long grain that was planted in four statewide locations in 2020. This line had an average yield of 9,320 pounds/acre at RES and 10,460 pounds/acre statewide. It outperformed L-207 by 2.4%

18Y1024 is a regular long grain planted for the second time in 2020. Average yields were 8,030 pounds/acre at RES and 10,030 pounds/acre statewide. The line did not outperform the regular long grain checks.

17Y1087 is another regular long grain with stem rot resistance in its background. It showed moderate stem rot resistance with good yield. Average yield was 10,046 pounds/acre at RES and 9,777 pounds/acre statewide.

Short grains

The short grains project includes conventional short grains and specialty types such as waxy rice, low amylose short grains, waxy short grains, Arborio types, and premium short grains. 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 34% premium quality short grains, 30% waxy or sweet rice, 23% conventional short grains, 9% low amylose short grains, and 4% Arborio or bold short grains. A total of 360 crosses were made in 2020, 253 populations at second generation were drill-seeded and evaluated, and 7,370 progeny rows at third to fifth generations were water-seeded and evaluated. In the preliminary yield trial, 65 lines were evaluated, 154 lines were in advanced yield tests, and eight lines were entered in statewide yield tests.

Statewide yield test performance

Commercially grown short grain varieties are used as checks or benchmarks for trait improvements in selection and advancement of experimental lines. Check varieties include S-102, S-202, Calhikari-202, Calmochi-101, Calmochi-203, Calamylow-201, and 89Y235.

Average grain yields were based on pooled results from six statewide locations and three RES maturity group experiments. S-202 yielded the highest at 9,922 pounds/acre, followed by CM-203 at 9,804 pounds/acre. CA-201 and 89Y235 had the lowest yields at 7,330 pounds/acre and 7,318 pounds/acre, respectively. Other average yields included S-102 at 8,332 pounds/acre, CH-202 at 8,032 pounds/acre, and CM-101 at 7,858 pounds/acre.

CH-202 had the highest amount of lodging at 84%. S-202 lodged 60% and CM-203 lodged 44%. Lodging may be attributed to heavy panicles or other environmental factors. Time to 50% heading included 76 days for 89Y235, 82 days for S-102 and CM-101, 85 days for S-202, and 86 days for CM-203 and CH-202.

S-202 and CM-203 have wide adaptation, with highest yield potential in Butte County. CM-101 has stable but low grain yields across all areas. S-102 also is adapted to all locations, but yields best in Butte County. Calhikari-202 is best suited to cooler environments such as in Yuba, Yolo, and Sutter counties.

Promising conventional short grains

S-202 was released as an early maturing, very high-yielding regular short grain in 2019. It consistently outperforms S-102 in all experiments at all locations.

S-202 averaged 10,147 pounds/acre at RES and 9,922 pounds/acre at all statewide locations in 2020. One conventional short grain, 18Y117, also outperformed S-102 in all RES experiments. Grain yield for this line was 9,820 pounds/acre at RES, compared to 10,147 pounds/acre for S-202. Across all statewide locations, average yield for 18Y117 was 9,924 pound/acre and 9,922 pounds/acre for S-202, not significantly different. However, 18Y117 has better adaptation than S-202 in the early warm environment of Glenn and Colusa counties. In these locations, S-202 averaged 8,800 pounds/acre, while 18Y117 yielded 9,725 pounds/acre. It also showed better yield than S-202 in Yuba County. Both have similar seedling vigor, cold tolerance, and susceptibility to stem rot. Lodging percentage is lower in 18Y117, and it is better adapted than S-202 in Glenn and Colusa counties. In these locations, S-202 averaged 8,800 pounds/acre, while 18Y117 yielded 9,725 pounds/acre. It also showed better yield than S-202 in Yuba County. Both have similar seedling vigor, cold tolerance, and susceptibility to stem rot.

In addition to 18Y117, seven other conventional short grain lines in the advanced yield trial proved promising. Grain yield ranges from 10,200 pounds/acre to 10,700 pounds/acre.

Premium short grains

Calhikari-202 (CH-202), genetically derived from the Japanese variety Koshihikari, is the most recent premium short grain rice in California. It has excellent cooking and eating qualities, but also has high lodging potential and relatively lower yield compared to other short grains.

One line, 17Y2087, is very promising and has consistently yielded higher than CH-202 since 2018. In 2020, it averaged 9,448 pounds/acre, compared to 7,982 pounds/acre for CH-202. In all statewide locations, 17Y2087 significantly outperformed CH-202 with its highest yield recorded in Yolo County at 10,265 pounds/acre. In Glenn and Colusa counties, where CH-202 has poor adaptation, 17Y2087 offered an additional 23 sacks of yield—a 35% advantage over CH-202. 17Y2087 showed better seedling vigor and lower lodging potential, as well as similar cold tolerance and stem rot resistance.

Milling yield harvested at different moisture contents, indicated that 17Y2087 averaged 65/72 (head/total) milling yield at 19% moisture content, while CH-202 had an average of 64/71 milling yield.

Rice samples of 17Y2087 were sent to marketing companies for evaluation. Thus far, Japanese evaluators indicate that 17Y2087 has excellent cooking and taste qualities similar to Koshihikari and is suitable for the premium quality rice market. Further head row purification and experimental seed increase is being proposed for future release of this high-yielding premium quality short grain.

Five additional lines averaged 10,036 pounds/acre to 10,763 pounds/acre. Seedling vigor for these lines is equal to or better than CH-202, with excellent lodging resistance. While these lines are very promising, further evaluations for grain and cooking taste qualities are needed to qualify for statewide yield trials in 2021.

Waxy short grains

Sweet or waxy rice is characterized by its stickiness, softness, and sweetness. Calmochi-101 (CM-101) and Calmochi-203 (CM-203) are commercially grown waxy rice varieties in California. They are used as checks to measure performance of promising new sweet rice varieties.

CM-203 continues to outperform CM-101 with an average statewide yield of 9,723 pounds/acre. Nine promising lines in the advanced trial yielded more than 9,500 pounds/acre. Five of these show no lodging. One promising line, 19Y2023, yielded 9,854 pounds/acre.

Low amylose and Arborio

Low amylose short grains are ideal for bento box rice, as they stay soft and taste good even after a period of refrigeration. Cooked rice is shiny, creamy, but less sticky than waxy rice. Since the release of Calamylow-201 (CA-201) in 2006, the Rice Experiment Station has not released a new low amylose variety. Foundation seed production of CA-201 ended in 2015. Breeding for lines in this segment continues on a small scale.

In 2020, one promising line, 16Y2028, was tested in all locations of the statewide advanced experiments. CA-201 had a mean yield of 7,330 pounds/acre, while 16Y2028 averaged 9,414 pounds/acre, a 29% yield advantage. However, it flowers seven days later than CA-201 and has lower lodging resistance.

Additionally, four more low amylose lines had grain yield more than 9,000 pounds/acre in the advanced trial at RES. One line, 20Y2130, yielded 10,405 pounds/acre. All four lines are more lodging resistant than CA-201 and 16Y2028.

Despite its small niche market and the uncertainty of acreage for Arborio rice, breeding efforts continue. For comparison, 89Y235 is used as a check, with grain yield of 7,318 pounds/acre. It was planted only at RES. It has high seedling vigor, lodges by 35%, is cold tolerant, and is susceptible to stem rot.

Two lines were entered in preliminary yield trials. The line 18Y2069 was evaluated in two locations in Butte County and at RES. Another line, 18Y2070, was entered in very early statewide experiments in Sutter, Yuba, and Yolo counties and at RES. Both of these lines have higher yield potential than the check but flower 12 to 13 days later. Between the two, 18Y2070 is a better choice with grain yield of 9,050 pounds/acre. It also has moderate resistance to stem rot.

Disease resistance breeding

The short grains project aims to incorporate resistance to stem rot and blast in all short grain types. Using some medium grains carrying blast resistance genes, 58 crosses were made to transfer resistance into short grains. USDA-derived seeds such as Kamenoo and Aichi Asahi were also used to transfer additional blast resistance genes. Previous crosses are now in the third generation.

With the support and DNA marker capacity of the genetics lab, more than 4,000 third generation individual plants from various short grain types were tested for the presence of blast resistance genes with linked markers. Lines containing the desired blast resistance genes are being grown in the greenhouse and will be advanced into progeny rows in 2021.

For stem rot resistance, a line designated as 14Y3143 was used in 2018 short grain crosses. Additional crosses were made in 2019 and 2020 with medium and long grains that showed resistance to stem rot in 2018 field evaluations. Crosses made for stem rot resistance will be evaluated when these lines enter the advanced yield trial.

Environmental stress tolerance

Environmental stress resilience is another area targeted for inclusion into all short grains. In 2019, preliminary evaluations for cold, salinity, and drought stresses were conducted during the seedling stage. Medium and long grain varieties were included in these tests.

Evaluations of salinity and drought stress were conducted in the greenhouse, while cold stress evaluation took place in a refrigerated growth chamber. All plants were scored visually. Some varieties showed encouraging levels of tolerance to the three abiotic stressors. The experiments were repeated in the summer of 2020 to confirm observations.

The analysis shows that cold tolerance is ubiquitous in RES varieties, especially in short grains and medium grains. Long grains have moderate cold tolerance. The majority of short, medium, and long grains are sensitive or highly sensitive to salinity—except for Calhikari-201, M-105, M-207, and Calaroma-201, which showed moderate salt tolerance. Varieties CS-S4, M-103, L-202, and A-301 showed good levels of drought tolerance. Additionally, S-201, S6, L-204, and Calmati-201 showed moderate drought tolerance.

Stem rot evaluation

To support the medium, short, and long grain projects in the development of varieties with stem rot resistance, rice pathology experiments continued in a limited capacity. In 2020, a total of 2,565 rows were inoculated and evaluated in the stem rot nursery. Out of these, 187 are entries from statewide yield trials, 547 are from advanced yield trials, 58 are released RES varieties, and 183 are recombinant inbred lines from a gene mapping study.

Results of this evaluation show that stem rot resistance is very rare in RES breeding lines despite years of effort. In fact, the majority of varieties and germplasm released by the station are susceptible or highly susceptible to stem rot. Only the check germplasm 87Y550 showed high resistance. For short grains, S-102 and CH-202 showed moderate resistance to stem rot. For long grains, L-201 and Calmati-201 also showed moderate resistance. All medium grains were susceptible or highly susceptible to stem rot.

From the 187 statewide entries, only two medium grains showed resistance similar to 87Y550. From the advanced yield tests, three lines were resistant. Only five resistant lines were identified in the mapping population. Further genotyping these five resistant lines will help in the identification of DNA markers for future stem rot resistance selection.

Disease survey

The weather in 2020 allowed for early planting, followed by insignificant precipitation until harvest time. However, smoke and haze from wildfires in September and October coincided with grain filling as rice matured. Those hazy days likely contributed to high temperature and high humidity, leading to little or no disease observance in yield plots and the surrounding rice fields of the six statewide testing locations inspected September 3. Although disease observance in 2020 was not significant at RES, precaution and appropriate field management will continue.

Quarantine introductions

In participation with the Uniform Regional Rice Nursery (URRN) of the Southern U.S. rice breeding programs, RES continues to receive and provide field evaluations of Southern breeding materials. In 2020, a total of 145 lines were received—52 from the University of Arkansas, 27 from Louisiana State University, 42 from Mississippi State University, 10 from Texas A&M, and 14 from the Missouri Rice Council. The majority of these entries are regular or Clearfield® long grains with few medium grains and no short grains. Seeds were processed for the brown rice protocol in the pathology lab. Healthy seedlings showing no disease were transplanted to the greenhouse and were monitored through maturity. All but four lines passed the quarantine protocol. Harvested clean seeds were stored in the cold room for 2021 field evaluation.

Genetics laboratory

The new 2,200 square-foot Rice Genetics Building (formerly the DNA marker laboratory) became fully operational in March 2020. The name change reflects the larger role it now plays in the research activities of the station. Specific activities include marker-aided selection for the different projects; fingerprinting and testing the purity of advanced lines and RES-released rice varieties; and generating mutant populations using both irradiation and chemical mutagenesis. Since 2015, it has also been involved in the herbicide resistance project, generating mutant populations and mapping genes and developing DNA markers.

Marker-aided selection

Screening materials for blast resistance, grain quality, aroma, and herbicide resistance are common functions at the genetics lab. Highlights of this work include:

• 3,960 lines were screened for different blast resistance genes in the medium grains project and 4,736 in the short grains project.

• 1,672 lines were screened for aroma in the medium grains project to potentially introduce some value-added traits.

• 4,400 early generation advanced ROXY® lines, head rows, seed maintenance rows, and progeny rows were analyzed for herbicide tolerance.

• 14,768 lines were screened using DNA markers for aroma, blast resistance, and oxyfluorfen tolerance traits.

DNA fingerprinting

A key function of the rice genetics lab is to assess the identity and purity of varieties and lines. About 3,080 lines from the breeding program were assessed for purity.

In one case, growers in Glenn County reported that rice plants in an M-210 field were infected with blast, but DNA fingerprinting revealed that the submitted samples were actually M-209, which does not have the resistance gene. Speculation is that this may have been the result of an overflight from a neighboring field.

In another case, seed growers requested the identity of a variety planted in a large acreage. In another instance, growers suspected mislabeled seed lots. The seeds headed differently from their expected maturity profile. Fingerprinting work in the genetics lab ascertained the varieties planted in these fields.

Off-types growing in an aromatic rice field also were submitted for analysis. DNA results revealed the field was contaminated by a variety that was not an RES-bred variety.

Herbicide tolerance

The lab has performed mapping studies of oxyfluorfen resistance in a mutant population of M-206 to determine the gene or genes responsible for the resistant phenotype. Studies over the last six years show the source of this resistance in a specific gene inside chromosome 5. The mechanism of tolerance is unique, stemming from three independent mutations in the rice.

Planting crews water seed rice through an aluminum trough.
Approximately 40,000 rows are planted in the RES breeding nursery in about six days.

All information on the genetics of oxyfluorfen resistance and identification of the the genes responsible for tolerance has been submitted in a patent application under review. To support the patent application, the genetics lab has used CRISPR (a non-GMO technology). In 2020, CRISPR-derived plants were further characterized and showed that this technology can successfully be used to control oxyfluorfen resistance in rice. While a promising technology, CRISPR is very labor intensive and time consuming. Therefore, RES will continue to rely upon traditional pedigree methods alongside gene editing methods.

Herbicide tolerant rice

ROXY® is a heritable non-GMO rice trait that provides tolerance to the post-patent herbicide ALB2023 (oxyfluorfen) and has been recovered in the variety M-206, California’s most widely grown Calrose variety. The trait is controlled by a single recessive gene and is a new mechanism for rice herbicide tolerance.

Lines from a backcross to M-206 (17Y3000) and M-210 (19Y4000) have been increased and purified. They have been analyzed in yield tests from 2017 through 2020. Agronomic and quality performance observations show that these lines are not significantly different from M-206.

Six years of research in multiple locations shows that the herbicide applied preplant in a water-seeded system provides high levels of rice weed control with the ROXY® trait. It is also effective in drill-seeded rice with a preplant and preflood application and may have potential in other rice-growing regions.

A provisional U.S. patent was filed in 2016 and expanded upon in 2019, providing additional information on genes, mutation sequences, new data, and a biochemical pathway in support of the patent application. A response from the patent office is anticipated in 2021.

A shared partnership and commercial agreement has been reached with Albaugh LLC and the California Cooperative Rice Research Foundation (CCRRF). Submission to the federal Environmental Protection Agency for herbicide registration in rice with concurrent review by the California Department of Pesticide Regulation will be made by Albaugh in 2021. Target commercial production for what will be known as the ROXY® Rice Production System is 2023.

The breeding program has focused initially on developing an herbicide tolerant Calrose medium grain. Experimental lines 17Y3000 and 19Y4000 will be considered for foundation seed increase in 2021.

ROXY® field research and demonstration was extensive in 2020, including six Albaugh off-station efficacy experiments. However, cancellation of Rice Field Day and group tours last year because of the pandemic prevented this work from being presented and shared with growers.

Breeding with genomic selection

Almost all the national and international rice breeding programs use conventional breeding schemes—the pedigree method, a very time-consuming approach. Advances in molecular genetics have been incorporated into plant breeding programs in recent years. However, this approach is limited by the small number of useable molecular markers.

A new approach called genomic selection shows enormous potential to significantly enhance breeding efficiency and is being integrated into the RES rice breeding program. In 2018, a rice population was developed to analyze the variability of all the advanced lines from the previous five years. This “training population” consists of 360 lines, including 210 medium grains, 64 long grains, 73 short grains, and 13 compound grain types. All the varieties released by RES are included in this population, capturing most of the diversity in the RES breeding program. The training population was transplanted at RES in 2019 for line purification, seed multiplication, and agronomic study.

In 2020, a drill-seeded field plot experiment was conducted with the training population. Yield and other agronomic traits were taken. Milling data also was recorded. Average yield was 10,672 pounds/acre and ranged between 5,523 pounds/acre and 13,680 pounds/acre, which shows the large diversity in the population. Percent head rice ranged between 20.4% and 71.1%, with an average head rice yield of 61.43%. Average harvest moisture was 16.8%.