Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization.

Rice grain shape is a major determinant of rice market value and the end-use. We mapped quantitative trait loci (QTL) for grain shape traits in a bi-parental recombinant inbred line population (Trenasse/Jupiter) and discovered two major grain length QTLs-qGL3.1 and qGL7.1. Previously, a major grain shape gene GS3 was reported in the qGL3.1 region and grain length gene GL7 was reported to be encompassing qGL7.1 locus. The re-sequencing SNP data on the International Rice Research Institute (IRRI) 3K Rice Genome Project (RGP) panel were obtained from the IRRI SNP-Seek database for both genes and haplotype diversity was characterized for each gene in this diverse panel. United States rice germplasm was not well represented in the IRRI 3K RGP database. Therefore, a minimum SNP set was identified for each gene that could differentiate all the characterized haplotypes. These haplotypes in the 3K RGP panel were screened across 323 elite U.S. genotypes using the minimum SNP set. The screening of haplotypes and phenotype association confirmed the role of GS3 under qGL3.1. However, screening of the GL7 haplotypes in the U.S. germplasm panel showed that GL7 did not play a role in qGL7.1, and in addition, GL7.1 did not segregate in the Trenasse/Jupiter RIL population. This concluded that qGL7.1 is a novel QTL discovered on chr7 for grain shape in the Trenasse/Jupiter RIL population. A high-throughput KASP-based SNP marker for each locus (GS3 and qGL7.1) was identified and validated in elite U.S. rice germplasm to be used in an applied rice breeding program.

Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs.

The potential of genomic selection (GS) to increase the efficiency of breeding programs has been clearly demonstrated; however, the implementation of GS in rice (Oryza sativa L.) breeding programs has been limited. In recent years, efforts have begun to work toward implementing GS into the Louisiana State University (LSU) Agricultural Center rice breeding program. One of the first steps for successful GS implementation is to establish a suitable marker set for the target germplasm and a reliable, cost-effective genotyping platform capable of providing informative marker data with an adequate turnaround time. The objective of this study was to develop a marker set for routine GS and demonstrate its effectiveness in southern U.S. rice germplasm. The utility of the resulting marker set, the LSU500, for GS applications was demonstrated using four years of breeding data across 7,607 experimental lines and four elite biparental populations. The predictive ability of GS ranged from 0.13 to 0.78 for key traits across different market classes and yield trials. Comparisons between phenotypic selection and GS within biparental populations demonstrates similar performance of GS compared with phenotypic selection in predicting future performance. The prediction accuracies obtained with the LSU500 marker set demonstrates the utility of this marker set for cost-effective GS applications in southern U.S. rice breeding programs. The LSU500 marker set has been established through the genotyping service provider Agriplex Genomics, and in the future, it will undergo improvements to reduce the cost and increase the accuracy of GS.

A SNP marker set was developed for genomic selection in southern U.S. rice breeding programs. Predictive ability across target germplasm was shown with 3 yr of data (4,078 lines). Within-population predictive ability was shown across four biparental populations. Genomic and phenotypic selection ability to predict future performance was compared.

Identification and mapping of a novel resistance gene to the rice pathogen, Cercospora janseana.

KEY MESSAGE: The genetic architecture of resistance to Cercospora janseana was examined, and a single resistance locus was identified. A SNP marker was identified and validated for utilization in U.S. breeding germplasm Cercospora janseana (Racib.) is a fungal pathogen that causes narrow brown leaf spot (NBLS) in rice. Although NBLS is a major disease in the southern United States and variation in resistance among U.S. rice germplasm exists, little is known about the genetic architecture underlying the trait. In this study, a recombinant inbred line population was evaluated for NBLS resistance under natural disease infestation in the field across three years. A single, large-effect QTL, CRSP-2.1, was identified that explained 81.4% of the phenotypic variation. The QTL was defined to a 532 kb physical interval and 13 single nucleotide polymorphisms (SNPs) were identified across the region to characterize the haplotype diversity present in U.S. rice germplasm. A panel of 387 U.S. rice germplasm was genotyped with the 13 haplotype SNPs and phenotyped over two years for NBLS resistance. Fourteen haplotypes were identified, with six haplotypes accounting for 94% of the panel. The susceptible haplotype from the RIL population was the only susceptible haplotype observed in the U.S. germplasm. A single SNP was identified that distinguished the susceptible haplotype from all resistant haplotypes, explaining 52.7% of the phenotypic variation for NBLS resistance. Pedigree analysis and haplotype characterization of historical germplasm demonstrated that the susceptible haplotype was introduced into Southern U.S. germplasm through the California line L-202 into the Louisiana variety Cypress. Cypress was extensively used as a parent over the last 25 years, resulting in the susceptible CRSP-2.1 allele increasing in frequency from zero to 44% in the modern U.S. germplasm panel.

Haplotype Characterization of the sd1 Semidwarf Gene in United States Rice.

CORE IDEAS: Genomic data from diverse germplasm used for application in targeted breeding germplasm. Six SNPs identified that can characterize all haplotypes present at SD1 locus in diverse rice. Three alleles of the SD1 gene identified in US rice germplasm including two semidwarf alleles. Two SNPs identified and validated that differentiate the SD1 allele present in US germplasm. KASP assays designed for both SNPs for use in high-throughput breeding applications. Plant height is an important target in US rice (Oryza sativa L.) breeding programs and the large effect of the sd1 semidwarf gene makes it a suitable target for marker-assisted selection. Although the deletion underlying the semidwarf allele is known and a gel-based DNA marker is available, this marker is not ideal for applied breeding because of throughput and cost constraints. The objectives of this study were to characterize the haplotype diversity at the SD1 locus within US rice germplasm and develop a single nucleotide polymorphism (SNP) assay for breeding applications. The International Rice Research Institute (IRRI) SNP-Seek database was used to characterize the haplotype diversity present at the SD1 locus across a set of rice accessions and seven haplotypes were identified. The US rice germplasm was not well represented in the IRRI database, so a set of six SNPs was identified that could differentiate all detected haplotypes. These SNPs were designed into Kompetitive allele specific polymerase chain reaction (KASP) assays and screened across 359 elite US genotypes. Of the seven haplotypes, two were present within the US germplasm, one of which was the semidwarf deletion allele. A third haplotype was observed within the US medium-grain germplasm and demonstrated to be a semidwarf allele derived from the induced mutation in the 'Calrose76'. Two SNPs were identified that distinguish the three SD1 haplotypes present in the US germplasm. These SNPs were validated across the US germplasm and two biparental populations.