Recipient Organization
SOUTH DAKOTA STATE UNIVERSITY
PO BOX 2275A
BROOKINGS,SD 57007
Performing Department
(N/A)
Non Technical Summary
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 >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 & 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 hybrid 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 on the 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 used to 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.
Animal Health Component
50%
Research Effort Categories
Basic
(N/A)
Applied
50%
Developmental
50%
Goals / Objectives
Goal #1: Seed dormancy (SD) is an adaptive trait of both ecological and agricultural important. Lack of SD often causes pre-harvest sprouting (PHS) in cereal crops, resulting in loss of yield, reduction in grain qualities or inadequate germination of commercial seeds, while excessive SD could lower germination uniformity of crop cultivars and cause feral plants or weed problem. It has long been a challenge to manipulate cereal crops for the dormancy level that is sufficient for the resistance to PHS but does not cause the weed problem. The dormancy trait is controlled by multiple genes, which have been mapped as quantitative trait loci (QTL) in cereal crops in the past >20 years. Many of the loci, including those on the same chromosomal segments, have been finely mapped and tagged with molecular markers to facilitate selection of the QTL alleles. Balancing selection, which occurs in natural populations to maintain genetic diversity at multiple loci for such a complex trait as SD, can be modified for crop breeding to meet the challenge. Thus, the first goal of this project is to extend the balancing-selection theory to crop breeding to improve the resistance of cereal crops to pre-harvest sprouting using the mapped QTL alleles.Goal #2: Rice (Oryza sativa) is a major cereal crop and a model plant for grass species as well. Rice varieties are inbred or hybrid, with the latter higher in yield potential than the former. Limiting factors for hybrid rice are high price and inadequate (<70% or 80%) germination of hybrid seeds. The rice crop in US distributes mainly in the South-Central States, where hurricanes and rainfalls in the summer to fall seasons often trigger PHS or on-plant germination. Thus, it is important to improve the PHS resistance to increase germinability or lower farmers' cost for hybrid seeds. Genetic and technical reasons for the inadequate germination include: 1) currently used male-sterile (MS) and fertility restoration (RF) lines of hybrid rice lack sufficient SD to prevent hybrid seeds from germination on the plants; and 2) seed producers apply the gibberellin (GA) hormone to MS plants to promote panicle emergence from the leaf sheath to increase the yield of hybrid seeds, which could also induce on-plant germination and lower seed vigor or storability. Thus, the second goal of this project is to extend the balancing-selection theory to rice breeding by integration of linked GA-insensitive SD genes into the MS and RF lines to improve the quality and germinability of hybrid seeds.Weedy rice (O. sativa) is a rich source of SD genes. A major QTL, qSD12, accounted for most of the genotypic variation for SD between weedy and cultivated rice and was finely mapped onto a genomic region of 100 kb. Map-based cloning detected three tightly linked genes (SD12a, b & c) underlying qSD12, with all the functional alleles (ABC) derived from a rare accession of weedy rice and the non-functional alleles (abc) common in modern cultivars. The ABC and abc unbalanced haplotypes were used to dissect the coupling linkage into the balanced haplotypes Abc, aBc, abC and ABc. Isogenic lines (ILs) for the balanced and unbalanced haplotypes, together with commercial MS and RF lines, have been selected to accomplish the two project goals. The project objectives are stated in the following sections.Objective 1: To model balancing selection for the linked SD12a, b and c loci in an isogenic background of rice.Balancing selection in this project refers to a mating design for multiple loci, each with two contrast alleles linked in repulsion, such as the Ab and aB haplotypes. This design can be used to manipulate the dormancy level of hybrid F1 (e.g., Ab//aB) seeds and reduce transgressive segregation, or extremely dormant genotypes (AB//AB) that combine effect-increasing alleles from both parents, in the F2 populations. Frequencies of the transgressive segregants vary with linkage strengths and effect sizes of the genes. The SD12a, b and c loci locate on a genomic segment of 80 kb, with SD12a and b next to each other (<4 kb apart) and SD12b and c separated by a tandem structure of 6 transposable elements (TEs). Thus, a series of experiments are designed to estimate: 1) recombination fractions between any two of the SD12a, b and c loci; 2) frequencies of transgressive segregation for the SD12s in the F2 seed populations; and 3) main (additive & dominance) and epistatic effects of the three genes.Objective 2: To introduce one, two or three of the SD12s into a male-sterility (MS) system and evaluate their effects on seed vigor and germinability in response to the GA application.Hybrid seeds are developed on the MS plants. We attribute the inadequate germination of hybrid seeds to their weak dormancy, side effects of MS genes on the panicle enclosure and hull dehiscence, and a side effect of GA application (to promote the panicle emergence) on germination initiation on the plant. Embryo dormancy delays germination and could mitigate the side effects. Thus, breeding experiments are designed to introduce a series of SD12s into a CMS system, to evaluate their mitigating effects on germination and to determine the number of genes suitable to maintain a high-level germinability of hybrid seeds.Objective 3: To introduce a subset of SD12s into an elite fertility-restoration (RF) line and evaluate their effects on pre-harvest sprouting.An RF line is the male parent of a hybrid variety and contributes a haploid genome to the hybrid to restore its male fertility and generate heterosis. Integration of a subset of SD12s (e.g., abC) into an RF line to complement with the subset in an MS line (e.g., ABc//ABc) can improve resistance of the abC//abC inbred line to PHS and germinability of the ABc//abC hybrid seeds and minimize the dormant extreme (ABC//ABC; freq. <0.002429 in Fig. 9B) in the F2 generation. Thus, experiments are designed to integrate a subset of the linked genes, such as the aBc, abC and ABc haplotypes, into a commonly used RF line and evaluate the resistance of new RF lines to PHS.Objective 4: To evaluate the SD12-containing male-sterility and fertility-restoration lines for combing abilities and heterosis in an Arkansas breeding program.The recipients of SD12s are commonly used MS or RF lines to develop hybrid varieties, because they outperform in general (GCA) and/or specific (SCA) combing abilities with genetically distant partners to produce heterosis for abiotic/biotic stress resistances, agronomic traits, and ultimately the yield. Compared with pyramiding genes from different chromosomes, introduction of linked genes as a haplotype into parental lines of a hybrid variety could help maintain their combining abilities to maximize the heterosis. Thus, experiments are designed to evaluate the SD12-containing CMSA and RF lines for GCA and SCA with breeding lines annually selected from an established rice breeding program at the University of Arkansas and to enhance the rice germplasm and develop new varieties of hybrid rice.
Project Methods
Objective 1: To model balancing selection for the linked SD12a, b and c loci in an isogenic background of rice.To model balancing selection for the linked SD12a, b and c loci. isogenic lines (ILs) developed for the balanced haplotypes in the previous research are being used to develop hybrid F1s and F2 populations. The populations will be genotyped with DNA markers on a high-resolution map for the SD12-containing region to estimate recombination fractions between SD12a and b, SD12b and c, or SD12a and c. Progeny lines of the recombinant F2s, together with the ILs for the balanced and unbalanced haplotypes, will be grown in a controlled environment to evaluate seed dormancy by standard germination testing, and the germination data used to estimate main and epistatic effects of the three genes. The genotyping and phenotypic data will be combined to model the linkage strengths, the speed of linkage disequilibria (LD) decay across generations, and the occurrence of extremely dormant genotypes in the F2 seed populations from different crosses.Objective 2: To introduce one, two or three of the SD12s into a male-sterility (MS) system and evaluate their effects on seed vigor and germinability in response to the GA application.To introduce the SD12(s) into a male-sterility system, a series of isogenic lines for one, two or three of the dormancy genes have been crossed with a cytoplasmic male-sterility maintaining (CMSB) line, the hybrids will be backcrossed (BC) with the CMSB line, genomic/marker-assisted selections will be used to advance the recurrent backcrosses to synchronized the genetic background, and plants that containing the SD12(s) will be selected from the advanced generations as new SD12-containing CMSB lines. The CMSB lines will be crossed with the male cytoplasmic male-sterile (CMSA) line (the CMSB sister line) to select new SD12-containing CMSA lines from the hybrid F2 populations. The new CMSA and CMSB lines, together with the new RF lines, will be evaluated for: 1) the degree of seed dormancy of the parental lines; 2) seed vigor, storability (aging-tolerance), and germinability of hybrid (F1) seeds from the CMSA plants (female parents) in a controlled environment; and 3) germination responses of the hybrid F1 seeds to the GA applications at flowering.Objective 3: To introduce a subset of SD12s into an elite fertility-restoration (RF) line and evaluate their effects on pre-harvest sproutingTo introduce a subset of s into an elite fertility-restoration (RF) line,Objective 4: To evaluate the SD12-containing male-sterility and fertility-restoration lines for combing abilities and heterosis in an Arkansas breeding program.To evaluate the SD12-containing male-sterility and fertility-restoration lines for combing abilities and heterosis, hundreds of tester lines will be selected from advanced generations of >300 crosses and ~600 F2-F6/BC populations, currently available in an Arkansas rice breeding program to cross with the SD12-containing CMSA or RF lines, including those selected from the BC2, F3, F4 generations. The hybrid F1s, together with their parental lines, will be grown in the same field environment and evaluated for agronomic traits and yield components using a completely randomized block design, and data collected from the field experiments will be used to estimate general and specific combining abilities and heterosis for the yield components and yield. Additional crosses will be made with newly selected breeding lines and field experiments for the combining ability analysis continued during the project period to identify promising combinations between the new CMSA and RF lines. The selected parental combinations will be further tested for heterosis and the dormancy degree and germinability of the hybrid seeds to select new hybrid varieties.