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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS Title: Putative fissure-resistance QTLs mapped to chromosomes 1 and 8 based on allelic frequency differences observed between fissure-resistant and fissure-susceptible progeny from two segregating populations

item Pinson, Shannon
item Gibbons, James -
item Jia, Yulin
item Yeater, Kathleen

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: March 7, 2012
Publication Date: February 1, 2013
Citation: Pinson, S.R., Gibbons, J., Jia, Y., Yeater, K.M. 2013. Putative fissure-resistance QTLs mapped to chromosomes 1 and 8 based on allelic frequency differences observed between fissure-resistant and fissure-susceptible progeny from two segregating populations. 35TH Rice Technical Working Group Meeting Proceedings, February 27, - March 1, 2012 Hot Springs, Arkansas. CDROM

Technical Abstract: Whole rice kernels have two to three times more market value than broken, which means that any reduction in milling yield results in financial losses for both rice producers and millers. One of the primary causes of rice breakage during milling is fissuring of the rice before it even enters the mill. A common cause of rice fissuring is the exposure of drying, mature kernels to humid field or postharvest conditions that cause the outer layers of the kernels to reabsorb moisture and swell, creating an inward pressure on the endosperm that can cause it to crack. Rain and dew are common causes of rice field-fissuring. ‘Cypress’, a southern U.S. variety released in 1993, is known for its resistance to kernel fissuring, but is not grown widely today, having been replaced with cultivars having higher yield potential and disease resistance. While breeders would like to incorporate Cypress’ fissure resistance into improved cultivars, their efforts have been limited due to a lack of methods for identifying and selecting for fissure-resistance in early breeding generations. Marker assisted selection is based on the principle that when markers linked to the genes affecting a desired trait are selected for the physically linked gene(s) and conferred trait are also in the selected individuals. But the reverse also holds true. The present study was accomplished by selecting for fissure resistance (FR) versus fissure susceptibility (FS) phenotype in two populations, then identifying molecular marker alleles that were present in different proportions within and between the FR and FS subgroups. A laboratory method wherein small samples of seed are evaluated for fissure rates after exposure to controlled rewetting conditions was used to divergently select for the 10% most FR and the 10% most FS progeny among 300 Cypress × ‘LaGrue’ F2 progeny, then F3 progeny testing conducted in both TX and AR, two replications per State was used to verify the F2 phenotypic selections. The laboratory evaluation method was also used to select 30 FR and 30 FS lines from among 280 Cybonnet × Saber recombinant inbred lines (RILs) that were grown and then progeny tested in four replications over two States. With fewer chances for recombination, linkage blocks are larger in F2 progeny than in RILs. The larger the linkage blocks in a mapping population, the fewer markers are needed to tag the genome and identify statistically significant marker-trait linkages. Therefore, we first characterized the FR and FS Cypress × LaGrue F2 progeny for 85 SSR markers scattered throughout the rice genome with a maximum marker gap of 30 cM, then characterized the Cybonnet × Saber RILs for markers on chromosomes 1 and 8 in order to cost-effectively verify and map in greater detail the fissure-resistance loci detected on these two chromosomes.Strong linkage between semidwarf plant height and FR was identified while conducting F3 progeny testing to verify the divergent FR and FS Cypress × LaGrue F2 selections. Cypress (FR) is semidwarf while LaGrue (FS) is tall, making segregation for height among the F2 and F3 progeny anticipated. What was not anticipated was that all of the FR F3 progeny were of semidwarf height, while mostly tall but also some short F3 progeny were noted among the FS selections. This suggested that at least one of Cypress’ FR genes is linked to the sd1 allele on chromosome 1. Since the sd1 gene was detected among some of the FS progeny, however, it also suggested that to achieve the strong FR exhibited by Cypress, this FR gene required assistance from at least one other FR gene located elsewhere in the genome. The present marker analysis of FR and FS Cypress × LaGrue F2 selections confirmed linkage disequilibrium for a section on the end of the long arm of chromosome 1 that contained the known location of the sd1 gene. Marker disequilibrium was also detected on a region of chromosome 8. The FR and FS Cybonnet × Saber RILs were then characterized for markers in these two chromosomal regions, and linkage disequilibrium in this second population confirmed the presence of FR loci on these two chromosomes. It is important to note that both Cybonnet and Saber are semidwarf in height do to the sd1 allele. If the association between sd1 and FR had been noted only among the Cypress × LaGrue progeny, it would have suggested that FR was associated in some way with the short stature and/or other plant architectural changes associated with the sd1 gene. However, the fact that analysis of the Cybonnet × Saber RILs also indicated linkage between markers near sd1 and FR without segregating for sd1 or plant height suggested instead that a FR gene is linked to but not allelic with the sd1 locus. The entire set of 280 Cybonnet × Saber RILs were then characterized for SSR markers along both chromosomes 1 and 8 so that the location of the FR loci could be determined more precisely by using multiple interval mapping analysis, conducted using QGene software. This analysis placed LOD peaks for FR between RM404 and RM22952 on chromosome 8, and suggested the existence of two FR loci on chromosome 1, one between RM6292 and RM104 near but distal to the position of sd1, and another on the short arm of chromosome 1, near RM580.

Last Modified: 8/24/2016
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