SNP Haplotypes: Unveiling the Truth of Past Relationships

Authors: McClung, Anna; ZHAO, K - Cornell University; DECLERCK, GENEVIEVE - Cornell University; Eizenga, Georgia; ALI, M. LIAKAT - University Of Arkansas; BUSTAMANTE, CARLOS - Cornell University; MCCOUCH, SUSAN - Cornell University

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/15/2010
Publication Date: 11/5/2010
Citation: Mcclung, A.M., Zhao, K., Declerck, G., Eizenga, G.C., Ali, M., Bustamante, C.D., Mccouch, S.R. 2010. SNP Haplotypes: Unveiling the Truth of Past Relationships. Rice Technical Working Group Meeting Proceedings. P. 43.

Interpretive Summary:

Technical Abstract: Over the last ten years, molecular markers have been widely accepted as a breeding tool for crop improvement. Currently, microsatellite markers are being used in rice to select for several simply inherited traits like components of cooking quality and a number of major genes linked to resistance to blast disease. In addition, markers are used to verify true crosses in a rice breeding program, facilitate selection of true breeding seed sources prior to release of a new cultivar, and fingerprint a cultivar for identity preservation. Markers have been used to survey historical cultivars found in the US rice pedigree and these revealed the inheritance of genes in current cultivars that are identical by descent from landraces originally introduced into the US over a century ago. Funding from USDA AFRI during 2004-2009 for RiceCAP extended the development of microsatellite markers from those linked with simply inherited traits to quantitative trait loci associated with sheath blight resistance and milling quality. Continued technological advances have resulted in faster throughput and greater marker saturation accompanied by rapidly diminishing costs of genotyping each year. In 2005, as a result of an international research collaboration, the japonica rice variety, Nipponbare, became the first crop genome to be completely sequenced. Subsequently, the indica cultivar 93-11 was sequenced, allowing detailed comparison of the genetic differences between these two representatives of indica and japonica rice; the two major varietal groups which are the basis for most of the commercially grown rice in the world. In 2008, another international collaboration, the OryzaSNP Project, resulted in re-sequencing of 20 world cultivars representing all five sub-populations found in Oryza sativa. This data set served as the basis for identification of 1536 single nucleotide polymorphisms (SNP) that were used by our group as part of an NSF funded project on rice diversity to develop an automated SNP assay and evaluate a panel of ~400 diverse O. sativa cultivars representing all five sub-populations and 100 O. rufipogon accessions. The genome scans revealed large linkage blocks common to each of the sub-populations as well as regions of chromosomal introgression between sub-populations. For example, in the tropical japonica material from the US, clear indica introgressions on chromosomes 1 and 12 were observed that were associated with the semidwarf gene (originating from Dee Geo Woo Gen) and the Pi-ta blast resistance gene (originating from Tetep), respectively. This information provides breeders with insights into marker assisted selection strategies that will conserve genomic regions or facilitate recombination. The 1536 “SNP chip” was also used in collaboration with the RiceCAP project to evaluate approximately 400 elite cultivars from all of the US rice breeding programs. This analysis demonstrated that US breeding programs each have relatively unique genepools, although some cultivars represent a synthesis of multiple genepools. Such detailed genomic information will be useful to breeders to help identify the best cultivars for crossing to maximize genetic recombination within the relatively narrow US germplasm base. In addition, it can be used “in hindsight” to track how recombination and selection occurred during cultivar development. For example, the 1536 SNP assay was used to compare Cypress and its two parentals, Lemont and L202. It revealed that large portions of chromosome 8 in Cypress were very similar to Lemont, whereas much of chromosome 4 was like L202. In contrast, chromosome 3 in Cypress demonstrated significant recombination between the two parental lines. Although the 1536 SNP chip provided greater marker saturation than previously available, it also demonstrated that there are large linkage blocks within US germplasm that ap