** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** A. RATIONALE OF THE PROJECT: CEREAL CROPS PRODUCE 90% OF ALL CULTIVATED SEEDS AND THE PRODUCTION HAS BEEN NEGATIVELY IMPACTED BY THE PRE-HARVEST SPROUTING (PHS) PROBLEM. THE SPROUTING IS THE ON-PLANT GERMINATION INDUCED TO NONDORMANT GENOTYPES (VARIETIES) BY HUMID ENVIRONMENTS BEFORE HARVESTING AND FREQUENTLY CAUSED LOSS OF YIELD, REDUCTION IN GRAIN QUALITIES, OR INADEQUATE GERMINATION OF COMMERCIAL SEEDS. GENETIC IMPROVEMENT OF THE RESISTANCE TO PHS HAS BEEN FOCUSED ON IDENTIFYING GENETIC RESOURCES AND GENES/QUANTITATIVE TRAIT LOCI (QTL) FOR SEED DORMANCY (SD) IN THE WHEAT, RICE, AND BARLEY CROPS IN THE PAST &GT;20 YEARS. IN AGRICULTURE, EXCESSIVE SD COULD CAUSE UNUNIFORM GERMINATION OF CROP CULTIVARS, FERAL PLANTS AND WEED PERSISTENCE. THUS, FURTHER EFFORTS INCLUDE PYRAMIDING THE QTL ALLELES IN A VARIETY TO MANIPULATE THE SD LEVEL, WHICH IS SUFFICIENT FOR THE RESISTANCE TO PHS BUT IS NOT HIGH ENOUGH TO CAUSE THE GERMINATION AND WEED PROBLEMS.RICE (ORYZA SATIVA) IS A MAJOR CROP IN THE WORLD, INCLUDING THE SOUTH-CENTRAL STATES WHERE HURRICANES AND RAINFALLS IN THE SUMMER TO FALL SEASONS OFTEN TRIGGER PHS. RICE VARIETIES ARE INBRED OR HYBRID, WITH THE LATTER HIGHER IN YIELD POTENTIAL THAN THE FORMER. A HYBRID VARIETY IS A HETEROZYGOUS (F1) GENOTYPE FROM A CROSS BETWEEN TWO INBRED LINES FOR MALE-STERILITY (MS) OR FERTILITY RESTORATION (RF). THUS, GENETIC IMPROVEMENT FOR THE PHS RESISTANCE IS TECHNICALLY MORE COMPLICATE FOR HYBRID THAN FOR INBRED VARIETIES, AS THE FORMER INVOLVES THE SD MANIPULATION FOR BOTH MS AND RF LINES TO MAINTAIN THEIR COMBINING ABILITIES AND HETEROSIS (F1) AND TO MINIMIZE THE TRANSGRESSION SEGREGATION FOR EXTREMELY DORMANT F2 SEEDS AND FERAL PLANTS IN THE NEXT SEASON(S). B. GOALS OF THE PROJECT: BALANCING SELECTION IS A THEORY IN EVOLUTIONARY BIOLOGY TO EXPLAIN HOW NATURAL SELECTION FOR SUCH AN ADAPTIVE TRAIT AS SD TO MAINTAIN GENETIC DIVERSITY AND REDUCE THE PHENOTYPIC EXTREMES IN POPULATIONS ACROSS GENERATIONS. THE GOALS OF THIS PROJECT ARE TO EXTEND THE BALANCING-SELECTION THEORY TO CROP BREEDING TO MANIPULATE THE SD AND OTHER ADAPTIVE TRAITS AND TO IMPROVE THE RESISTANCE OF INBRED VARIETIES TO PHS AND THE GERMINABILITY OF HYBRID SEEDS IN THE RICE CROP.C. OBJECTIVES OF THE PROJECT: THE PREVIOUS RESEARCH IDENTIFIED A MAJOR QTL (QSD12) ASSOCIATED SPECIFICALLY WITH EMBRYO DORMANCY IN RICE. MAP-BASED CLONING OF QSD12 IDENTIFIED THREE UNDERLYING GENES (SD12A, B &AMP; C), WITH THE FUNCTIONAL ALLELES FROM A RARE ACCESSION OF WEEDY RICE LINKED IN COUPLING (ABC) AND THE NON-FUNCTIONAL ALLELES (ABC) COMMON IN RICE CULTIVATED RICE. THE WILD- AND MUTANT-TYPE UNBALANCED HAPLOTYPES WERE ISOLATED INTO THE SAME BACKGROUND (ABC//ABC) AND DISSECTED INTO THE BALANCED HAPLOTYPES ABC, ABC, ABC AND ABC TO ACCOMPLISH THE ABOVE-STATED PROJECT GOALS. SPECIFIC OBJECTIVES OF THIS PROJECT ARE: 1) TO MODEL BALANCING SELECTIONS FOR THE SD12A, B AND C LOCI IN AN ISOGENIC BACKGROUND OF RICE; 2) TO INTRODUCE A SERIES OF SD12S INTO A MS SYSTEM TO IMPROVE H,YBRID SEED VIGOR AND GERMINABILITY; 3) TO INTRODUCE A SUBSET OF THE SD12S INTO A RF SYSTEM TO IMPROVE ITS RESISTANCE TO PHS; AND 4) TO EVALUATE THE SD12-CONTAINING MS AND RF LINES FOR COMBINING ABILITIES AND HETEROSIS IN A PUBLIC BREEDING PROGRAM IN THE ARKANSAS (AR) STATE.D. EXPECTED RESULTS: RESULTS FROM THE FIRST OBJECTIVE WILL INCLUDE: 1) RECOMBINATION FRACTIONS BETWEEN SD12A AND B, SD12B AND C, AND SD12A AND C; 2) MAIN (ADDITIVE AND DOMINANCE) AND EPISTATIC EFFECTS OF THE THREE GENES ON THE DEGREE OF SEED DORMANCY OR GERMINATION DELAY; AND 3) FREQUENCIES OF TRANSGRESSION SEGREGATIONS FOR EXTREMELY DORMANT GENOTYPES FOR TWO OR THREE OF THE LOCI IN THE F2 POPULATIONS. RESULTS FROM THE SECOND AND THIRD OBJECTIVES WILL INCLUDE: 1) NEW LINES WITH ONE, TWO OR THREE OF THE SD12S IN THE GENETIC BACKGROUND OF A COMMERCIAL MS LINE; 2) NEW LINES WITH A FUNCTIONAL ALLELE AT THE SD12A, B OR C LOCUS IN THE GENETIC BACKGROUND OF A COMMERCIAL RF LINE; AND 3) DATASETS FOR EFFECTS OF THE SD12S ONTHE PHS RESISTANCE IN THE MS OR RF BACKGROUND AND THE GENES' EFFECTS ON SEED VIGOR, STORABILITY AND GERMINABILITY OF HYBRID F1S BETWEEN THE MS AND RF LINES. RESULTS FROM THE FOURTH OBJECTIVE WILL INCLUDE: 1) HUNDREDS OF HYBRID F1S FROM CROSSES BETWEEN THE ISOGENIC LINES FOR THE SD12S AND BREEDING LINES SELECTED FROM THE AR BREEDING PROGRAM; 2) DATASETS COLLECTED FROM THE F1S ON GENERAL AND SPECIFICAL COMBINING ABILITIES AND HETEROSIS FOR AGRONOMIC TRAITS AND YIELD COMPONENTS; AND 3) NEW BREEDING LINES SELECTED FOR THE ENHANCED RESISTANCE TO PHS FROM ADVANCED GENERATIONS OF THE CROSSES. IN ADDITION TO THE GENETIC INFORMATION AND MATERIALS, THIS PROJECT WILL TRAIN AT LEAST ONE POSTDOCTORAL AND TWO DOCTORAL GRADUATE SCIENTISTS E. ANTICIPATED IMPACT: THE RESULTS FROM RESEARCH ON THE FIRST OBJECTIVE WILL REVEAL GENETIC AND GENOMIC STRUCTURES OF THE MULTIGENIC QTL, SUCH AS LINKAGE STRENGTHS, REGIONAL RECOMBINATION HOT/COLD SPOTS AND GENIC EFFECTS. THESE LINES OF INFORMATION WILL BE USEDTO ELUCIDATE EVOLUTIONARY MECHANISMS OF SEED DORMANCY AND OTHER ADAPTIVE TRAITS IN RICE, TO PREDICT THE DECAY OF LINKAGE DISEQUILIBRIA OF THE THREE DORMANCY GENES ACROSS GENERATIONS IN WILD RICE OR IN LOCALLY ADAPTED POPULATIONS OF WEEDY POPULATIONS, AND TO ESTIMATE FREQUENCIES OF TRANSGRESSION SEGREGATION FOR THE DORMANCY GENES IN BREEDING POPULATIONS. THE RICE PLANT HAS BEEN A RESEARCH MODEL FOR THE GRASS FAMILY. THUS, THE KNOWLEDGE GAINED FROM THIS PROJECT CAN BE USED TO INFER EVOLUTIONARY MECHANISMS FOR SEED DORMANCY IN THE OTHER CEREAL CROPS OR GRASS SPECIES.THE RESULTS FROM THE OTHER THREE OBJECTIVES ENHANCE GERMPLASMS OF THE RICE CROP, INCLUDING: 1) THE ISOGENIC LINES FOR UNBALANCED AND BALANCED HAPLOTYPES IDENTIFIED FROM THE PRELIMINARY AND ON-GOING RESEARCH; 2) NEW MS AND RF LINES WITH THE ENHANCED RESISTANCE TO PHS; AND 3) HUNDREDS OF BREEDING LINES WITH ONE OR MORE OF SD12S IN GENETIC BACKGROUNDS OF LOCALLY ADAPTIVE VARIETIES. SOME OF THE BREEDING LINES COULD BE DIRECTLY USED,TO DEVELOP NEW HYBRID VARIETIES.