Recent advances in whole genome sequencing (WGS) have allowed identification of genes for disease susceptibility in humans. The objective of our research was to exploit whole genome sequences of 13 rice (Oryza sativa L.) inbred lines to identify non-synonymous SNPs (nsSNPs) and candidate genes for resistance to sheath blight, a disease of worldwide significance. WGS by the Illumina GA IIx platform produced an average 5× coverage with ~700 K variants detected per line when compared to the Nipponbare reference genome. Two filtering strategies were developed to identify nsSNPs between two groups of known resistant and susceptible lines. A total of 333 nsSNPs detected in the resistant lines were absent in the susceptible group. Selected variants associated with resistance were found in 11 of 12 chromosomes. More than 200 genes with selected nsSNPs were assigned to 42 categories based on gene family/gene ontology. Several candidate genes belonged to families reported in previous studies, and three new regions with novel candidates were also identified. A subset of 24 nsSNPs detected in 23 genes was selected for further study. Individual alleles of the 24 nsSNPs were evaluated by PCR whose presence or absence corresponded to known resistant or susceptible phenotypes of nine additional lines. Sanger sequencing confirmed presence of 12 selected nsSNPs in two lines. "Resistant" nsSNP alleles were detected in two accessions of O. nivara that suggests sources for resistance occur in additional Oryza sp. Results from this study provide a foundation for future basic research and marker-assisted breeding of rice for sheath blight resistance.
The initial discovery of cytoplasmic male sterile (CMS) three-line system made it possible to produce hybrids that significantly increase rice yields compared to its inbred counterparts. Further genetic and molecular studies help elucidate the mechanisms involved in CMS male sterility. Additional CMS types were also discovered with similar genetic control from wild sources by interspecific hybridization. While the three-line system was a success, the two line system using photoperiod genetic male sterile (PGMS), thermosensitive genetic male sterile (TGMS) and photoperiod and thermosensitive genetic male sterile (PTGMS) were becoming more popular due to the ease in breeding and with more hybrid combinations generated compared to the CMS types. Inheritance and molecular studies showed that the trait is controlled by one or more recessive genes depending on the genetic background and environmental conditions. Due to the sensitivity of the lines to temperature and/or photoperiod, unique breeding procedures were followed. Methods involved the use of growth chamber, timing of planting, and selection of suitable locations. These practices successfully maintained sterility for hybrid seed production or reversion to fertility for seed multiplication of parental male sterile lines.
Two‐line hybrid rice (Oryza sativa L.) breeding in the United States and China uses photoperiod/thermosensitive genetic male sterility (PTGMS) to produce lines with fertile or sterile pollen, depending on temperature and/or daylength. Although studied in China for >30 yr, genetic analysis of PTGMS in US environments is lacking. We therefore conducted genetic studies of male sterility over 3 yr in five F2 and BC1F2 populations derived from PTGMS line 2008S in Louisiana and Arkansas. Chi‐squared analyses in all populations indicated that sterility was controlled at both locations by two or three recessive genes. Inheritance and expression of PTGMS was found to be influenced by the particular combination of population and year (environment). Sequence comparisons of two regions in PTGMS loci LOC_Os07g12130 and LOC_Os12g36030 from six fertile and sterile lines revealed a diagnostic single‐nucleotide polymorphism (SNP) at each locus. Two‐way ANOVA in two F2 populations inferred that interaction of the two SNP‐containing regions contributed up to 65% variation for sterility in one Louisiana environment. Selective genotyping of the 2008S/CL131 F2 population detected new quantitative trait loci with R2 values ranging from 5 to 27% using single‐marker and composite‐interval mapping. Results from this study indicate that 2008S can be used as parental material for development of two‐line hybrids in Louisiana and Arkansas, but extensive testing of populations across years and locations will be required.
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