Rice Breeding Program, 2016

 

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 14 public varieties and basic seed of one Japanese premium quality variety were produced on 140 acres at the Rice Experiment Station (RES) in 2016.

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 oversees premium quality and short grains breeding. Farman Jodari leads the long grain project and also has served as liaison with Southern U.S. breeding programs. He has been working at RES since 1999 and will be retiring in 2017. Paul Sanchez is in charge of the rice pathology laboratory and will assume the role of Southern U.S. liaison when Jodari retires. 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.

RES Director Kent McKenzie concluded a three-year project that could lead to herbicide tolerant rice through induced mutation. That project successfully established protocols for generating and screening mutant populations and evaluating promising mutants for potential commercial application. Lines were developed from an M-206 population that showed a high level of tolerance to the herbicide oxyfluorfen.

Progress highlights from 2016 are reported below.

Breeding nurseries

Seeding of the 2016 breeding nursery began April 27 and was completed May 23. A total of 1,419 crosses were made for rice improvement, bringing the total to 47,915 since 1969. Crosses made in early spring 2016 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 2016 RES breeding nursery occupied approximately 70 acres. Water-seeded yield tests included 7,438 small plots and 3,318 large plots. The nursery included about 64,000 water-seeded and 11,160 drill-seeded rows and plots. Second-generation populations from 2014 and 2015 crosses were grown in precision drill-seeded plots on 10 acres. An estimated 150,000 panicles were selected from various second-generation populations for screening and advancement. Also in 2016, headrows of M-205, Calmochi-203, M-206, Calmati-202, and L-207 were grown for breeder seed production. Headrow seed can be used for several years to produce breeder seed because it is stored under low temperature and proper humidity conditions.

Selection and harvest of the 2015–2016 Hawaii winter nursery was completed and seed returned to RES for planting in May. The 2016–2017 winter nursery included 8,970 progeny rows planted October 25-26, 2016 and 600 first-generation crosses transplanted November 15, 2016. Selection and harvest was set for April 2017, 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 six-acre, drill-seeded nursery included 4,800 rows, and four acres of second-generation populations. Stand establishment and weed control was good. Some blanking was observed in the rows and in the second-generation populations.

Statewide yield tests

Statewide yield tests were conducted in grower fields and at RES in 2016 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 586 entries and check varieties. Yields of the top experimental lines compared well with check varieties. Superior entries are being advanced to 2017 statewide yield tests.

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.

The main goal of the medium grains breeding project is to develop new rice varieties with high and stable grain and milling yields without sacrificing the excellent grain quality of the Calrose varieties. 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 in Lihue.

CHECK VARIETY PERFORMANCE

Calrose varieties that are still in commercial production in California are used as checks in preliminary and advanced yield tests. These include M-105, M-205, M-206, M-208, and M-209. M-202, released in 1985, is no longer used in yield tests. M-104, though still commercially grown, is being gradually replaced by M-105. M-208 will be phased out as a check variety by 2018, as a new blast resistant line is being considered for release.

M-209, released in 2015, is the top-yielding check variety, registering an average grain yield of 10,350 pounds/acre in 2016, compared to M-205 at 10,040 pounds/acre, and M-206 at 10,300 pounds/acre. The four-year average yield for M-209, M-205, and M-206 is 9,900 pounds/acre, 9,510 pounds/acre, and 9,500 pounds/acre, respectively. M-209 has the biggest overall grain size of the Calrose varieties and may have lower head rice yield if harvested at low moisture content. It is adapted to warmer areas and may not perform well in cooler rice growing areas.

Variety

Days to 50% heading

Height

(cm)

Number

of tillers

Calrose
(combined means)

84 97 41
Jupiter 97 93 38
Titan 92 90 39
CL271 95 91 38

The very early maturing variety M-105 performed well in 2016 because of favorable weather conditions. It registered an average yield of 10,160 pounds/acre and overall yield of 9,170 pounds/acre. M-105 is one of the best varieties in terms of head rice yield, although its grains are one of the smallest among the Calrose varieties.

In 2016, Calrose medium grain varieties were compared with medium grains from the South for their agronomic characteristics and grain quality. Jupiter and CL271 were bred in Louisiana, while Titan is a medium grain developed in Arkansas. Calrose medium grains grown in this test included M-104, M-105, M-205, M-206, M-208, and M-209. A delay in heading and shorter plant height is indicative of Southern medium grain’s poor adaptation to the cooler growing conditions in California. Milled grains of Calrose are also heavier, longer, and slightly wider.

12Y3097 CALROSE ADVANCED LINE

A blast-resistant advanced line, 12Y3097, is in the final stage of yield testing and grain quality evaluation. It has been recommended for foundation seed increase in 2017. This is an early, glabrous, high yielding blast-resistant Calrose medium grain. 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 intended as a replacement for M-208, which contained the Pi-z gene found to be ineffective against the new IB-1 blast strain.

In statewide testing from 2013 to 2016, 12Y3097 has undergone head row purification for the last two years. At the RES location, grain yield was 10,430 pounds/acre, compared to 10,300 pounds/acre for M-206 and 9,490 pounds/acre for M-208. The overall yield advantage of this new line, based on pooled data, was 2.7% over M-206 and 8.7% over M-208. 12Y3097 has lower seedling vigor and plant height compared to M-206 and M-208.

Compared to M-208, 12Y3097 performed better in San Joaquin, Butte, Glenn, Yuba, and Sutter counties, with the highest yield advantage of 10% registered in Yuba and San Joaquin counties. M-206 still performed better, though slightly, in remaining test locations. Grain attributes in terms of chalkiness, seed weight, and grain dimension are comparable to M-206 and M-208. The similarity in grain dimensions and appearance indicate that 12Y3097 can be comingled with other Calrose medium grain varieties. Starch and protein content are similar to M-206 and M-208.

OTHER ADVANCED LINES

A total of 31 medium grain advanced lines entered statewide tests in 2016—regular medium grains, blast and stem rot materials, and herbicide-tolerant mutant lines. M-205, M-206, and M-209 are the standard check varieties for the three maturity groups in statewide tests. Grain yield of M-209 was higher compared to other medium grain checks in the early and intermediate/late group, while M-105, with an average yield of 10,380 pounds/acre, did well in the very early group. Overall, the 2016 milling yields were lower compared to previous years.

VALUE ADDED TRAITS FOR CALROSE

The medium grains project has begun to explore the use of rice traits that may add value for a new rice product. One of the traits under consideration is aroma similar to that found in long grain aromatic rice or the jasmines. M-206 was used as the parent variety. Several backcross populations have been made and progenies have been isolated with DNA markers.

Genetic studies on stem rot resistance are continuing. Results of previous mapping studies are being confirmed. Genetic studies have also been conducted to characterize the Roxy herbicide-resistant gene. Crosses have been made to develop mapping populations to locate the gene. Whole genome sequencing of mutant lines and M-206 has also been performed. Multiple approaches will, hopefully, identify the gene.

RES 2020

In 2016, the medium grains project developed a plan called RES 2020 to review breeding goals and objectives by grain type, prioritization and allocation of resources, and personnel responsibilities. The intent of this plan is to strengthen the entire RES breeding program to meet the current, emerging, and future needs of the rice industry.

Premium quality and short grains

The premium quality and short grains project includes conventional short grains, low amylose short grains, waxy short grains, premium quality short grains, premium quality medium grains, and bold grains such as Arborio. New lines are bred and selected for improved and stable grain yield and yield related traits, milling and cooking quality, reduced delay in maturity and blanking from cold temperature, lodging resistance, very early to early and uniform maturity, short flowering duration, and resistance to diseases.

WAXY SHORT GRAINS

Calmochi-201 and Calmochi-203 performed as expected in 2016. Calmochi-203 had significantly higher grain yield than Calmochi-101 in all statewide yield tests in 2016. The seven-year grain yield average for Calmochi-203 was 9,780 pounds/acre—28% higher than the 7,640 pounds/acre average grain yield of Calmochi-101. Calmochi-203 had slightly lower seedling vigor, later heading, taller height, less lodging, comparable panicle blanking, and a 3% higher head rice percentage.

PREMIUM QUALITY SHORT GRAINS

Calhikari-202 (CH-202), released as a new premium quality short grain variety in 2012, continues to show high yield and quality.

Grain yields of CH-202 were significantly higher than CH-201 in five out of eight statewide yield test locations in 2016. The average grain yield of CH-202 across statewide yield tests was 9,150 pounds/acre. CH-202 continued to exhibit high head rice percentage, registering 66% in 2016 milling tests.

Three premium quality short grain lines were evaluated in statewide tests. 13Y2031 was evaluated in the very early maturing and early maturing groups. However, it was dropped because it was not within chalkiness parameters. Another line, 15Y202, in its first year as an entry, showed potential with high yield, grain quality, and taste qualities.

Mutation breeding of 26 early heading lines of Koshihikari were evaluated. The top five yielding mutants had an average heading 16 days earlier than Koshihikari. Average grain yield was 8,090 pounds/acre—1,500 pounds/acre more than Koshihikari. Rice samples of “eKosh” are undergoing quality and taste tests.

PREMIUM QUALITY MEDIUM GRAINS

Eight premium quality medium grains were evaluated in statewide tests in 2016. The outstanding selection was 12Y2175—producing significantly higher grain yields than M-402 in six of seven statewide test locations. Average yield was 10,220 pounds/acre for 12Y2175 and 8,540 pounds/acre for M-402.

Compared to M-401 and M-402, 12Y2175 had similar seedling vigor and earlier heading by at least 16 days in 2016. It was similar to M-402 in plant height and lodging, with M-401 being taller and having a higher lodging percentage. Cold temperature panicle blanking was 10% higher than M-402 but less than M-401. Its head rice percent was similar to M-401 at 61%. Averaged across 2015 and 2016, 12Y2175 was similar in chalkiness to M-401 but higher than M-402. This advanced line will undergo experimental seed increase in 2017.

CONVENTIONAL SHORT GRAINS

Four conventional short grain lines were evaluated in 2016 statewide yield tests, with 10Y2043 at the forefront after being evaluated in both the very early and early maturing groups. Average grain yield of 10Y2043 across eight statewide test locations in 2016 was 11,330 pounds/acre, which was 18% higher than S-102. Its six-year average from 2011 to 2016 was 10,310 pounds/acre, which was 18% higher than S-102.

Compared to S-102 in 2016, 10Y2043 had slightly lower seedling vigor, headed two days later, was slightly shorter, and had lower chalky area percentage. Furthermore, 10Y2043 is smooth, unlike S-102. 10Y2043 is being advanced to foundation seed increase in 2017.

LOW AMYLOSE SHORT GRAINS

In 2016, two low amylose short grain entries were evaluated, with 15Y2100 having a grain yield of 10,090 pounds/acre—29% higher than CA-201. It had high seedling vigor and headed three days later than CA-201.

ARBORIO OR BOLD GRAINS

The Rice Experiment Station has not yet released a bold grain variety, although it did release 87Y235 as germplasm in 1994. The development of new bold grain lines is a first step to promote interest in this type of rice. The lone bold grain entry into statewide yield tests in 2016 was 15Y2002. It has smooth grains and similar seedling vigor, heading, and grain yield compared to 89Y235.

BLAST RESISTANCE BREEDING

Blast resistant lines of the six grain types managed by this project were evaluated in 2016. Lines with grain yield higher than their respective check varieties included eight bold grains, 18 premium quality medium grains, eight conventional short grains, six low amylose short grains, seven premium quality medium grains, and five waxy short grains. Marker-assisted selection identified the blast resistant lines possessing combinations of four genetic makers. These genes confer broad-spectrum and complementary resistance to blast pathogen races.

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.

CONVENTIONAL LONG GRAINS

Plant breeder Farman Jodari is retiring in 2017 after leading the long grain program since 1999. Thank you Farman.

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 currently on milling yield and cold tolerance.

L-207 is a conventional long grain variety released in January 2016 that has shown grain yield and milling yield advantages over L-206. L-207 is an intermediate height and early maturing variety with Southern long grain cooking quality. It is two days later and 6 inches taller than L-206. Average grain yield in statewide tests during 2015 and 2016 was 10,300 pounds/acre, compared to 9,600 pounds/acre for L-206 and 9,610 pounds/acre for M-206.

At the Yolo test locations, L-207 compared favorably with L-206 and M-206—important because cooler locations have been a challenge for long grains. As a result, the areas of adaptation for L-207 include most areas of the state except for San Joaquin County.

Despite taller plant height, no significant lodging of L-207 has been observed. Milling yields at sequential harvest moistures continue to be monitored. Within a span of seven days, head rice yields remained stable—ranging between 63% and 67%.

Cooking quality of L-207 is similar to Southern long grains, with intermediate amylose, intermediate gel type, and moderate RVA profile. In 2012 to 2016 tests, L-207 showed significantly lower stem rot disease compared with L-206 and M-206. Aggregate sheath spot resistance also was tested on this line at the RES greenhouse from 2012 to 2014. Significantly higher resistance was observed in 2013 and 2014.

Another conventional experimental line, 14Y1006, tested significantly better than check varieties in very early and early maturity statewide locations. Average yields over 17 experiments were 10,600 pounds/acre for 14Y1006, 10,310 pounds/acre for L-207, 9,600 pounds/acre for L-206, and 9,610 pounds/acre for M-206. This experimental line is two to three days earlier and three inches shorter than L-207, with similar milling yield at 65%. Head row production of 14Y1006 is planned for 2017.

SPECIALTY LONG GRAINS

Expanded breeding efforts continued in specialty long grains, including jasmine, basmati, and conventional aromatics such as A-202.

In 2016, eight jasmine types were tested in statewide yield tests and 45 preliminary yield tests. Breeding objectives for jasmines include low amylose, strong aroma, a high degree of whiteness, and smooth cooked-grain texture. For a second year, 15Y84 has shown superior agronomic and quality characteristics. The two-year average yields over 11 experiments were 9,940 pounds/acre for 15Y84 and 9,340 pounds/acre for A-202. Milling yield for both entries was 60%. Feedback from marketing organizations has been favorable. Foundation seed production of 15Y84 is planned for 2017.

Several other jasmine selections were tested in early and intermediate/late statewide yield tests and are being advanced. Efforts in the area of conventional aromatics such as A-202 also continued in 2016. Two conventional aromatics—12Y1022 and 15Y1197—were evaluated in statewide tests. A considerable number of aromatic types are being generated from other populations.

A-202

A-202 is an early maturing conventional aromatic variety that was released in January 2014. It is intended as a replacement for A-301.

Compared to A-301, A-202 is nine days earlier, four inches taller, and has significantly higher seedling vigor. Average yield overall for early and intermediate locations in 2016 was 9,300 pounds/acre for A-202, compared to 10,300 pounds/acre for L-207.

Three-year average head rice yield for A-202 is 61%. Susceptibility of A-202 to stem rot and aggregate sheath spot is similar to A-301. Milled kernels of A-202 are slightly bolder than A-301. Amylose content, gelatinization temperature type, and starch profile are similar to A-301 and L-207. Subjective evaluations of cooked grain texture indicate that A-202 is slightly softer than L-206.

A-202 is susceptible to cold induced blanking (as is A-301) and is therefore not recommended for cooler locations. Areas of adaptation include Butte, Colusa, Yuba, Glenn, and Sutter counties.

BASMATI

Basmati breeding efforts also continued in 2016. Eight selections were examined in statewide yield tests and 26 selections in preliminary yield tests at the Rice Experiment Station. Basmati types, in general, are about 15% of the long grains nursery.

Average yield levels in early and intermediate/late statewide yield test locations was 6,500 pounds/acre. Average milling yield was 47%. Because of its extremely fine grain shape, basmati head rice yield is in the range of 50% to 60%. However, basmati provides a considerable market premium. Wholesale prices for imported basmati is more than three times that of standard rice.

Cooking quality evaluations of current basmati lines have shown considerable quality advantages over Calmati-202, a true basmati variety released in 2006. Cooked kernel elongation is an important characteristic for any basmati variety. Efforts are underway to improve cooked grain texture of basmati types. The effect of aging on texture and flakiness is being monitored on a select number of advanced entries.

Small experiments are being conducted to identify harvesting and processing procedures that can enhance milling yield and cooking quality. Factors include harvest moisture, drying rate, and milling degree. The goal is to continue to improve both grain and milling yields without losing any basmati quality attributes.

MILLING QUALITY

Continued improvement in milling yield and stability remains an important objective in the long grains program. Grain characteristics are being evaluated that will lend milling yield stability under adverse weather to allow for a wider window of harvest.

In 2016, all selections in the preliminary and advanced yield tests were evaluated in special plots for milling yield evaluation. Advanced lines were evaluated at six harvest moistures. Preliminary entries were tested at two harvest moistures. The goal for long grains is to maintain a minimum 65% head rice yield in advanced breeding lines.

DISEASE RESISTANCE

Stem rot resistance from the wild species Oryza rufipogon continues to be incorporated into an increasing number of high-yielding long grain lines. In 2016, 15 entries were tested in preliminary yield tests. Despite a close linkage between the stem rot resistance trait with increased chalkiness and cold susceptibility, selections are being obtained that have broken this linkage and have a combined low stem-rot score and low blanking. Efforts to improve the milling yield of stem rot-resistant lines are underway.

Rice pathology

Breeding for disease resistance is a cooperative effort between rice breeders and the RES plant pathologist. 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 few crosses were made to combine stem rot resistance and blast resistance. Molecular markers are being used to evaluate advanced lines with blast resistance genes.

STEM ROT

Screening for stem rot resistance included evaluations on 4,844 rows. Of these, 3,200 rows were wet seeded, resulting in less seed drift and the establishment of more uniform stands and allowing use of higher nitrogen levels without inducing lodging. Increased nitrogen results in greater disease severity and better screening opportunities.

Promising long- and short-grain resistant lines have emerged. Resistance was confirmed in some lines in 2016. Some lines, as in the past, have also shown resistance to sheath spot equivalent to that found in aggregate sheath spot-resistant donor parents.

In addition, 660 rows of a mapping population for identification of stem rot resistance genes derived from Oryza rufipogon were evaluated in the field at RES. Some materials identified as resistant in 2014 were again resistant in plots and rows, but many others were inconsistent due to lack of nursery uniformity.

Variations in stem rot ratings in 2016 were observed between and among lines in the mapping population. Intensive evaluation will be conducted in 2017 under controlled environment conditions inside the greenhouse to confirm the degree of susceptibility and resistance of selected lines.

Under field conditions, early maturing plants generally were found to be more susceptible to stem rot than late maturing plants. Very early maturing and tall plant entries were also more prone to lodging.

A modified stem rot rating scale and scoring system will be used for phenotyping in 2017. Combined with genotypic data derived from molecular markers, this will aid in the identification of lines with stem rot resistance.

AGGREGATE SHEATH SPOT

The backcross program aims to transfer aggregate 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 reference.

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

BLAST

Blast, first identified in California in 1996, was lower in severity and incidence from 1998 to 2009. Overall, blast was lower in severity and incidence between 2012 and 2016. A few affected fields continue to be found, mostly on the west side of the valley. M-104 appears to be more susceptible than other varieties, followed by M-205.

Seedlings of all statewide entries were screened against a mixture of the IG1 and IB1 blast races in the greenhouse. This test should confirm the presence or absence of blast resistance genes and provide information on the relative susceptibility of lines without major genes.

The backcross program also seeks to introduce resistance genes into M-206. Only genes with a wide spectrum of blast resistance in worldwide tests have been chosen. Seven backcrosses have been made and screened for blast resistance. Four of these lines were entered in the early statewide trial between 2012 and 2014. These lines yielded more than M-208 and even as much as M-206.

Blast infection has been found in some M-208 fields every year between 2009 and 2013. DNA testing confirmed that a new race of the fungus has been found. This new race is significantly different pathologically from IG1. Lines with different blast resistance genes from the M-206 backcross program were screened against M-208 isolates. Again, lines with the Piz gene and sometimes the Pik gene were susceptible. However, lines with other genes were resistant.

The components of M-208 were also tested individually. They are still resistant to the IG1 strain of the blast fungus but not the IB1 strain. It is too early to judge whether resistance has been overcome in M-208 since infection occurred in only one in 5,000 to one in 10,000 plants. The new race may be able to attack scattered M-208 plants, but it is unknown whether it will severely damage M-208 in the future.

A project by the DNA marker lab to screen for blast has been successful. Resistance genes have been pyramided into three lines and are being advanced for agronomic evaluation. These genes were chosen for their broad spectrum and complementary resistance to blast races. The presence of several resistance genes in a variety should prevent rapid loss of resistance when exposed to natural blast fungus populations.

More than 500 blast single spore IB1 isolates were taken from M-208, as well as typical IG1 isolates, and screened against three California varieties (M-205, M-206, M-208) and other international varieties. The isolates were subsequently screened on new monogenic and near-isogenic lines from the International Rice Research Institute. This work will help facilitate future screening efforts.

COMBINING RESISTANCE

An attempt to combine resistance to blast, stem rot, and aggregate sheath spot is in progress.

This effort involves a cross of a four-gene blast pyramid line with a stem rot-resistant line. It has undergone rapid generation advance with greenhouse disease screening for blast and stem rot. Second-generation populations were screened against blast in March 2016. Third-generation populations were screened against stem rot in June 2016, and the fourth-generation populations were screened against blast in November 2016. The fifth-generation populations will be screened against stem rot in the field in 2017.

A portion of the seed will be used in aggregate sheath spot screening in the greenhouse. Resistance was found in some lines evaluated in 2015. Further evaluation will take place in 2017. The goal is to identify well-performing lines with resistance to all three diseases.

QUARANTINE INTRODUCTIONS

The building blocks for any breeding program are varieties with traits desirable in commercial production. Two hundred lines from the southern U.S. were received for evaluation and use in the breeding program at the Rice Experiment Station. These were grown to full maturity and screened inside the greenhouse in summer 2016.

DNA marker laboratory

The DNA marker laboratory supports the different breeding programs and special projects. The lab is involved in marker-assisted 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 generation of mutant populations for herbicide resistance. In 2016, the lab also did fingerprinting work on red rice.

MARKER-ASSISTED SELECTION

Marker-assisted selection for both blast resistance and grain quality is now a routine part of work in the DNA marker laboratory. In 2016, a total 910 breeding lines from the medium- and short-grain projects were screened for blast resistance. A total of 2,419 long grain breeding lines were evaluated using five DNA markers for grain quality. And 992 lines from the medium grain project were evaluated for aroma, grain quality, and herbicide resistance. These materials are being advanced by the medium grain breeder.

DNA FINGERPRINTING

Another important function of the DNA lab is to assist in variety identity and purity assessment—DNA fingerprinting. The lab maintains a marker database of all rice varieties released from the Rice Experiment Station, as well as other rice variety introductions. The lab fingerprints advanced lines before they are recommended as varieties.

The lab has developed a panel of DNA markers that can distinguish California medium grains from each other. A similar panel is in development for short- and long-grain varieties.

In 2016, researchers conducted fingerprinting of various breeding materials for the medium grain project. About 2,080 lines, consisting of advanced breeding lines and seed maintenance lines, were assessed with different markers.

The long grain project requested 2,462 lines for fingerprinting—conventional long grains and advanced jasmine lines. The short grain project submitted 842 lines for fingerprinting, consisting of the advanced line 10Y2043, some elite lines, and early Koshihikari mutants. Fingerprinting data assures the breeders of the identity and purity of their materials.

SUMMARY OF MARKER WORK

A total of 8,275 lines were analyzed for all breeding projects at the Rice Experiment Station in 2016. This includes both marker-assisted selection (47%) and DNA fingerprinting (53%) work done in the lab. About 47% of the requests came from the long grain project, with 37% from the medium grain project and 16% from the short grain project.

HERBICIDE RESISTANCE

The Rice Experiment Station has embarked on a project to find herbicide resistant rice using induced mutation. A mutant resistant to the herbicide oxyfluorfen (Goal®) 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. Four other mapping populations were generated involving a cross of the short-grain line 09Y2179 with M-206 mutant lines 14G3, 14G4, 14G6, and 14G9.

A marker survey on A-202, M-206, and 09Y2179 examined 512 microsatellite markers. Marker data have been generated for each individual in the mapping populations. Genetic analysis zeroed in on the A-202/14G7 cross. It showed the location of the recessive gene for resistance to oxyfluorfen on a chromosome of interest. To identify the herbicide resistance gene, a multipronged approach is underway. Mapping and fine-mapping of the herbicide resistance—as well as sequencing the genome of both M-206 and mutants—are being pursued.

A fine-mapping population involving the cross of mutant 14G6 with L-206 was developed, and 1,116 individuals were analyzed. Fine-mapping work will continue to further refine the region of interest and narrow the number of candidate genes.

RED RICE RESEARCH

Reports of weedy red rice in fields across the state’s rice growing areas have been increasing. An extensive DNA marker analysis was done to help characterize California red rice samples. This will help create a better understanding of how many types of red rice are present and how they are distributed. The type of red rice present in a particular place and its relatedness can offer clues to origin and dispersal.

An initial study of 57 red rice accessions and select rice varieties has been initiated. Data for 84 markers were generated and analyzed. Altogether, more than 90 accessions were analyzed. The DNA marker analysis aligned these into 19 groups, formed into six clusters based on marker relationships, phenotype, and accession location. There are 20 markers that can be used to validate the groupings.

STEM ROT RESISTANCE

The goal of mapping stem rot resistance is to find a tightly linked marker that can be used in breeding programs. Work continues on mapping stem rot resistance, focusing on phenotyping disease symptoms. The plant pathologist is confirming whether lines identified as resistant in genetic studies present as well in greenhouse and field studies. Screening these lines several times for blast resistance will help to confirm chromosomal regions. Stem rot resistance in several chromosomes has been identified and is being further studied with the goal of finding a consistent DNA marker for resistance.