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United States Department of Agriculture

Agricultural Research Service

Title: Progress in Developing DNA Markers for Milling Yield

Authors
item Kepiro, Joseph
item McClung, Anna
item McClung, Anna
item Fjellstrom, Robert

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: December 1, 2003
Publication Date: June 1, 2004
Citation: Kepiro, J.L., McClung, A.M., Fjellstrom, R.G. 2004. Progress in developing dna markers for milling yield. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. 2004 CDROM.

Technical Abstract: Milling yield can vary considerably in rice cultivars, and cultivars with poor milling will often be rejected by rice growers. The cultivar Cypress has gained wide recognition for having high and stable milling yield over a variety of grain moisture levels. It would be greatly advantageous to be able to transfer this high milling yield of Cypress into advanced genetic lines that rice breeders are developing for future release. Identifying DNA markers associated with Cypress-type milling yield could allow efficient and cost effective marker assisted selection of lines with high milling yield potential. Two populations segregating for milling yield are being examined. Data has been collected for total percentage of grain and whole percentage of grain. The number of days to head and days to harvest was recorded along with harvest moisture and milling moisture. Grain dimensions of length (L) and width (W) were measured and the L/W ratio calculated. The first population is a progeny population of 117 offspring derived from a Cypress/Pelde advanced breeding line (with high milling potential) crossed to Jefferson (with moderate milling yield). The milling yields of progeny lines in this population range from 52.8 % to 66.2 % with two years of milling yield data. Fifty-eight SSR (simple sequence repeat) markers are scored in this population. A second population segregating for milling yield is a Cypress x Panda cross. Approximately 250 lines in this population have been analyzed for milling quality. The milling yields of progeny lines in this population range from 22.3 % to 64.8 % with one year of milling yield. The Cypress x Panda population has simpler parentage, is larger, and has a wider range of milling yield values than the Cypress/Pelde x Jefferson cross. Therefore, it has been chosen for detailed mapping and QTL (quantitative trait loci) analysis. Analyses to determine the percentage of amylose content and alkali spreading value have also been conducted for progeny lines of the Cypress x Panda population. Additional segregating markers are being identified for genetic mapping and QTL analysis. The strategy is to map the Cypress x Panda population with AFLP (amplified fragment length polymorphism) markers and use SSR markers with known locations to anchor the AFLP markers onto chromosomes. The Invitrogen/LifeTechnologies AFLP System II kit (with E+2 IRD-labeled primers, and unlabeled M+3 primers) is being used to generate AFLP markers from leaf extracted genomic DNA of parents and progeny. A Li-Cor 4200 genetic analysis system and multiplexed PCR enables analysis of two differently labeled primer combinations simultaneously by producing two separate images from a single gel. The AFLP system II will allow screening of 256 primer combinations, each producing approximately 100 scorable bands per gel image. Preliminary tests indicated that each primer combination (two per gel) is producing 2-4 scorable polymorphisms (4-8 per gel). Screening the primer combinations with two replicates of six progeny and the parents is will allow selection of primers that produce the highest quality markers (reproducible and scorable) and the maximum number of polymorphisms per gel. The map will be generated using JoinMap 3.0 for linkage analysis of markers from DNA extracted from a single plant of approximately 120 progeny lines in the population. QTL single locus analysis and interval mapping will be done using MapQTL 4.0 and utilize markers scored from a bulk of individuals in each line. The 117 lines and 58 SSR markers in the Cypress/Pelde x Jefferson population were analyzed for whole kernel percentage by single locus analysis using MapQTL 4.0. The WAXY locus (which controls grain amylose content) showed the highest significance in both years that data were collected. No other large effects were consistently observed, although some markers did show association with the percentage of whole kernels after milling. We are presently looking within amylose classes (fixed for the WAXY locus) for markers significantly associated with milling yield. Grain shape and dimension are also being investigated. Results will be presented for these QTL analyses and the progress in AFLP marker generation.

Last Modified: 10/25/2014