Rice Breeding Program, 2022


Rice Experiment Station, Administration and Plant Breeding Staff

The California Cooperative Rice Research Foundation (CCRRF) is committed to the development and release of excellent highyielding and high-quality rice varieties. The RES Breeding Program implements rice variety development for all market classes of long, medium, and short grains.

The focus of the RES rice breeding program is to develop improved rice varieties with high-yielding and superior-quality grain types and market classes that are commercially competitive in the world market for the benefit of California rice growers now and in the future.

The Rice Experiment Station is now up to full strength with the majority of positions filled. Dr. Harrell’s leadership has brought progress and stability. This year features the release of two new varieties: The long awaited herbicide resistant Medium Grain with the ROXY® technology, released as M-521 and a Premium Quality Short Grain, Calhikari-203

Breeding Nurseries

Three breeding nurseries are established to accelerate breeding activities. The breeding nursery locations include: (1) Rice Experiment Station facility in Biggs, CA (77,552 lines), (2) the Hawaii Winter Nursery for generation advance and seed increase in Lihue, HI (8,203 lines), and (3) the San Joaquin Cold-Tolerance Nursery for cold-induced blanking screening (4,165 lines).

Each of these nurseries has a unique role in the California breeding program. The RES facility allows for the creation of new varieties and summer seed production and evaluation. The Hawaii facility allows for a winter generation to be produced, giving the breeders two generations per year. The San Joaquin nursery evaluates the cold tolerance of varieties, and is used in conjunction with refrigerated greenhouses at RES.

Medium Grain

M-521 (19Y4000)

ROXY® Herbicide Tolerant Rice

The RES Rice Breeding Program initiated a special project in 2014 to bring non-GMO herbicide tolerant rice technology to California’s rice growers. After a successful breeding effort and patenting of the trait, a “shared partnership” and commercial agreement has been reached between Albaugh LLC and CCRRF on the commercial development and launch of ROXY® RPS. Albaugh will sell the post patent herbicide ALB2023 and ALB2024 (oxyfluorfen) for the ROXY® RPS system. Milestones thus far:

• Submission to EPA for herbicide registration for rice was made by Albaugh in 2021.

• Albaugh has been conducting multi-location efficacy testing throughout the California rice growing regions with rice weed control research groups and the UC since 2020. Trials will continue to help position and educate the market on performance, establish BMP’s and prepare the market for the 2024 launch of ROXY® RPS.

• Eight years of research involving multiple locations shows that ALB2023 applied preplant in a water-seeded system provides high levels of rice weed control with ROXY® rice.

ROXY® RPS offers several very attractive features for rice weed control:

• Oxyfluorfen provides a Group 14 (PPO) mode of action. This novel mode of action should help manage weed resistance to Group 1 (ACCase) and Group 2 (ALS) herbicides, which comprise three quarters of the herbicides registered on rice.

• ALB2023 in combination with the ROXY® trait provides early season control of yield robbing grass and broadleaf weeds, with activity on weed biotypes with proven resistance.

• Provides a new tool to broaden BMP’s in rice production and is compatible with most currently registered post emergence rice herbicides.

• The risk of damage to neighboring fields is minimal since conventional rice varieties have tolerance to the herbicide at low rates.

• The preplant application system allows for use in sensitive areas with adjacent crops.

RES 2022 Efficacy Testing

In the RES ROXY® nursery, ALB2023 herbicide rate studies gave very good weed control. The delay in rice emergence increased with rising ALB2023 rates to 6 days at the highest rate. 50% heading was three days later at the 2 and 2.5 pts/A rate.

Some have been following the progress of the herbicide tolerant ROXY® variety 19Y4000. The CCRRF Board approved the release of this variety and the new official name will be M-521. This line will be the first herbicide resistant, medium grain in California. The variety will have both oxyfluorfen and blast resistance. It was bred conventionally with the aid of marker-assisted selection (MAS) for Pi-b blast resistance and the ROXY® trait. The original cross was with M-210 (blast resistant) and the oxyfluorfen resistant discovery. Backcrossing with M-206 seven times has resulted in a variety 99.6% genetically similar to M-206.

Confidence in the productive ability of M-521 is high as it was evaluated in the UCCE State Wide (SW) Yield Tests for four years (2019-2022), for a total of 41 yield experiments. Based on the pooled four-year SW Yield Tests, field performance of M- 521 was similar to M-206 and M-210 in all SW test locations beginning in 2019. It has very good seedling vigor, flowered at 87 days, with a plant height of 96cm, and a lodging potential like M-206 and M-210. Yield performance of M-521 in different zones or UCCE test locations is summarized in the table below. Location specific performance indicated 2-4% yield advantage of M-521 over M- 206 and M-210 in San Joaquin and Biggs. In other locations, M-521 had an average of 2% lower yields than the two Calrose varieties.

Grain Yield
(lb/A, 14%
MC, 4yrs)
Yield over
Yioeld over
San Joaquin 9618 9502 9848 2% 4%
South Butte 9292 9578 9131 -2% -5%
Glenn 9152 9487 8885 -3% -6%
Colusa 9295 9178 9000 -3% -2%
Sutter 9200 9246 8748 -5% -5%
Yolo 9130 9067 8894 -3% -2%
Biggs 8752 8733 9018 3% 3%
North Butte 8624 8982 8882 3% -1%
Yuba 7860 7538 7334 -7% -3%
MEAN 8907 8949 8839 -2% -2%

Grain Characteristics and Milling Quality of M-521

The milled grains of M-521 were marginally lighter, slightly longer, and slightly narrower than the M-206, and M-210 varieties.

When cut at 22% moisture and above, M-206 had a head and total of 68/71, while M-210 and M-521 had 67/71. At 18-22% moisture, the milling yield of M-521 was slightly improved to 67/72, similar to M-210. As is typical, when harvested at moistures below 18%, all three entries tended to have reduced head rice as grains became drier.

RVA and Quality Evaluation of M-521

The average apparent amylose (20.66%) and protein content (5.96%) of M-521 was similar to M-206 and M-210. All three had low gel type typical of a Calrose-type medium grain. Based on the average of four-year RVA (rapid visco analysis) data, M-521 does not deviate significantly from the profile of M-206 or M-210. Results indicate that M-521 cooking characteristics are similar to M-206 and typical of a Calrose type rice.

Cold-induced Panicle Blanking and Disease Screening Tests

Cold tolerance screening is performed in San Joaquin and in the refrigerated greenhouse at RES from 2019 to 2022. Averaging the four-year results in San Joaquin shows that M-521 had blanking of 1.3%, compared to 1.5% for M-206 and 1.2% for M-210. Overall, in both San Joaquin and greenhouse testing, M-521 had a cold tolerance level similar to M-206 and M-210.

Based on the four-year stem rot resistance screening, M-521 had an average stem rot score of 3.38, which is moderately susceptible to stem rot disease. M-206 and M-210 were both susceptible to stem rot with scores of 3.77 and 3.45 respectively.

For blast resistance, screening is limited to the detection of incorporated blast genes using DNA markers detected by the RES Genetics Lab. M-521 and M-210 were both positive for the presence of the Pi-b blast gene, while M-206 was negative for the desired gene. Therefore, if a blast outbreak occurs, M-210 and M-521 are expected to show resistance.

Calhikari-203 (17Y2087) Premium Quality Short Grain Rice

17Y2087 is a semidwarf, early maturing, high yielding premium quality short grain rice approved for release in 2023. The new variety will be named Calhikari-203 (CH-203). It has a 11-13% yield advantage over CH-202 and CH-201, averaging 9,050 lb/A yield based on five-year UCCE SW yield tests. CH-203 consistently showed higher lodging resistance of 33% vs. CH-202 at 65% and CH-201 at 61%. CH-203 has high milling quality. Test evaluations indicated the excellent grain appearance, cooking, and taste qualities of CH-203 for the premium quality short grain market. Taken together, the attributes of CH-203 make it suitable for comingling with existing premium quality short grains or a viable alternative to CH-202 or CH-201.

CH-203 Yield and Agronomic Performance

Compared to CH-202 and CH-201, CH-203 had a similar seedling vigor, it flowered at 89 days which is two days later than CH-202, one day later than CH-201. CH-203 is considered semidwarf like the older Calhikari varieties at 90 cm plant height. It also has excellent straw strength as shown by the low lodging potential.

Performance of CH-203 in the cooler areas of Sutter, Yuba, Yolo, and San Joaquin, showed it to be cold tolerant as indicated by yields exceeding 10,000 lb/A in Yolo and San Joaquin. In Sutter and South Yolo, CH-203 had a 5-8% yield advantage over CH-202 & CH-201. In the low yielding site of Yuba, CH-203 had a 16% yield advantage.

In summary, CH-203 had a superior grain yield over CH-202 or CH-201 in all SW test locations. It is adapted in all rice growing counties of California that makes it a viable alternative rice variety for commercial rice production.

RVA and Quality Evaluation for CH-203

All three Calhikari lines had apparent amylose content of 20% and low gel type grain, indicating similar softness when cooked. Low protein content is desirable because low protein content is correlated to high taste scores. Two-year protein analysis indicated that CH-203 had lower protein content than CH-202 or CH-201.

Overall, the CH-203 cooking profile was similar to CH-202 and CH-201. The amylographic profile also show that CH-203 more closely overlaps the cooking curve of Koshihikari. Internal and external blind evaluations for grain appearance, cooking and taste qualities by mills, rice handlers, marketing organizations, and some Japanese evaluators indicated the close similarity of CH-203 to Koshihikari and CH-202.

Short Grain Breeding

Promising SPQ

In 2022, two high yielding, SPQ entries were identified (21Y2031 and 22Y2119) as potential candidates for SW yield tests in 2023. For grain yield, 21Y2031 showed a 17% yield advantage over CH-202 and CH-201. When 21Y2031 is harvested between 18-22% moisture, the milling yield averages 66/73% head and total. Analysis for chalkiness revealed more chalky kernels (3.2%) for 21Y2031 than CH-202 (1.0%) and CH-201 (2.4%). Compared to CH-202, it also had a higher taste score due to its lower protein content.

Line 22Y2119 is another SPQ that had good grain yield and quality performance. It had a 16% yield advantage over CH-202 and CH-201. Its grains were slightly more chalky (1.5%) than CH- 202 (1.0%), but less than CH-201 (2.4%). Lines 21Y2031 and 22Y2119 well be considered for SW yield test in 2023.

Promising Regular Short Grains (S)

Across the seven SW locations in 2022, 20Y2001 outyielded both S-102 and S-202. It averaged a yield advantage of 8% over S-202 and 28% over S-102. Compared to S-202 and S-102, line 20Y2001 was more adapted to different SW locations. Grain yield results show that it was the highest yielding line at six out of seven UCCE SW locations.

Milling yield of 20Y2001 was high compared to S-202 and had a similar percentage head rice to S- 102 when harvested at 18-22% moisture. It is later flowering, shorter than its sister varieties, and lodges more (46% vs 37-40%). Chalky grain percentages fall between S-202 and S-102. Disease screening data from 2021 at RES revealed high stem rot resistance with a disease rating score of 1.8 for the line.

Some future lines to keep an eye on would be 20Y2008 and 20Y2072. Both lines outyielded the standard check varieties at RES.

Promising Sweet Short Grains (SWX)

A waxy short grain line included in the SW yield test has been designated 20Y2124. Results show that 20Y2124 had an average yield advantage of 5% for CM-203, and 25% over CM-101. Although the average yield advantage was only 5% greater than CM-203, it had wider adaptation than either of the older varieties. Cold-induced panicle blanking results from the San Joaquin cold tolerance nursery, show 20Y2124 is cold-tolerant like CM- 203 and CM-101.

Genomic Selection

The Rice Experiment Station breeding program has successfully bred new and improved varieties for California growers using pedigree breeding method. The station also employs marker-assisted selection (MAS) for blast resistance, grain quality traits, and herbicide resistance. The whole variety development process takes about 10-12 years or longer, from the time the cross was made until variety release. While the pedigree method is proven effective, it is time-consuming, labor-intensive, and costly.

New breeding tools, such as genomic selection (GS), is emerging and may ensure complex traits are selected with improved accuracy and precision. GS, in principle, is another form of MAS. GS uses all markers spread across the genome to predict the performance of lines with genotypes only (organism’s genetic information) without phenotypes (observable physical traits). Thus, selections can be made earlier that reduce the number of candidates to be examined in the field.

The goal of the project is to integrate GS, as a complementary breeding tool to MAS, into the RES breeding program. This efficiency gain has three major steps:

• A population, that represents the genetic diversity of the RES breeding program, was assembled and field tested since 2020.

• A suitable marker set, that is cost effective and can discriminate the RES germplasm, will be developed for routine use genotyping GS materials (training set and predictive set).

• Assess the prediction accuracy of the GS prediction model for selecting complex traits.

A total of 360 lines, consisting of advanced breeding lines and released cultivars of all grain types, were selected to be phenotyped for grain yield and agronomic traits. These same lines were genotyped to form a training population. Broad-sense heritability estimates, based on the phenotype, ranged from 0.64 for seedling vigor to 0.88 for days to 50% heading. This indicates good predictability for the agronomic traits. Grain yield data will be gathered in 2023. In addition to field evaluation, the population will be genotyped with genomewide, single nucleotide polymorphism (SNP) markers to assess the potential of GS in the RES breeding program.

Long Grains

L-208 is the newest conventional long grain and was released in 2020. Agronomic characteristics, adaptation, milling, and cooking qualities of L-208 are similar to L-207.

Based on 2022 SW experiments, L-208 and L-207 had higher yield at locations outside of RES. The new variety, L-208, had approximately a 4.0% yield advantage over L-207 in 2022. It performed better and had higher yield in five out of seven SW experiments.

Promising Long Grain Lines

Three LG lines showed promise for future release: 19Y1018, 20Y1029, 20Y1008.

The advanced line 19Y1018 is a regular LG in the SW trials for a second time. It was planted in seven locations and out yielded L-208 and L-207 by 1.7% and 5.7%. Line 19Y1018 had less panicle blanking compared to Calaroma-201 in San Joaquin. Based on milling yield trends, the line showed stable head rice performance and can be harvested from 18-26% moisture content.

Genetics Lab

The main purpose of the RES Genetics Lab continues to be to provide the breeders with genetic marker information for the selection of potential and advanced lines as well as maintaining the purity of our released varieties. Throughout the year breeders submit leaf samples from F1, head rows, and ROXY® trait lines. Off-types that appear in RES or area producer’s fields are also genetically identified through marker analysis. Results from this year are:

• 2,497 parental and F1 plants were analyzed to determine true crossing.

• Head row purity was verified in over 3,700 samples which included short, medium, long, and specialty lines.

• The presence of the oxyfluorfen herbicide tolerant trait (ROXY®) was determined for about 765 plants whose response to the herbicide was atypical.

• With the eventual release of a ROXY® rice variety, an efficient and repeatable assay to identify the presence of the trait was developed. Overall, nearly 7,500 samples were processed, resulting in over 36,000 data points.

CRISPR technology

CRISPR technology has been used successfully in the lab to verify the oxyfuorfen resistant phenotype as well as to explore the targeting of other useful traits. An organism generated by CRISPR technology is considered a genetically edited organism and not a genetically modified organism. The difference is important in both consumer acceptance and government regulation. Genetically edited organisms do not have foreign DNA in their genome. A change in their phenotype is a result of a targeted change in their own DNA. This change could happen naturally and therefore is managed and regulated the same as conventionally bred organisms. The change in phenotype of genetically modified organisms is the result of the addition of DNA from another organism. This change could not happen naturally, so these organisms are managed and regulated in a stricter manner.

CRISPR technology is being developed and tested in the RES Genetics lab. No varieties are being released at this time. When CRISPR rice varieties are introduced in the future, it is hoped that RES will be able to enter the market in a timely manner.

Lab Improvements

In December 2020 CCRRF authorized the purchase of new analytical equipment for the RES Genetics lab. This will allow for the transition from SSR (simple sequence repeats) marker-based analysis to a SNP (single nucleotide polymorphisms) marker approach. The two techniques are similar in many ways which will result in a smooth transition. The difference is in the speed in which SNP maker results can be collected and analyzed. The running and identification of polymorphic alleles using SSR’s averages 3.5 hours with the equipment available in the lab. Whit the purchase and use of the plate reader and SNP markers the average time to identify polymorphic alleles will be less than 30 seconds.