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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #324669
Title: Association mapping of rice cold germination with the USDA mini-core

Author
item ZHAO, HAIJUN - Oak Ridge Institute For Science And Education (ORISE)
item McClung, Anna
item WANG, XUEYAN - University Of Arkansas
item Jia, Yulin

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 12/23/2015
Publication Date: 7/2/2017
Citation: Zhao, H., McClung, A.M., Wang, X., Jia, Y. 2017. Association mapping of rice cold germination with the USDA mini-core. Proc. 36th Rice Technical Working Group Meeting, Galveston, TX, p. 75-76. March 1-4, 2016. CDROM.

Interpretive Summary:

Technical Abstract: Assuring stand establishment is a critical first step in optimizing rice crop yields. Plant stand density can impact yield potential, incidence of some diseases, weed competition, and grain quality. Most rice production in the Southern USA is drill seeded in the spring. Planting can occur as early as February along the Gulf Coast and in March in the upper Mid-South area. Early planting is being driven by the desire to avoid fall inclement weather patterns on the Gulf Coast and interest in planting subsequent winter wheat crops in the upper Mid-South. Planting current rice cultivars early in the spring can result in yield losses due to delayed germination and slow seedling growth. Thus, breeders desire to have access to germplasm and genetic markers that can facilitate the development of new varieties that have cold tolerance at the planting stage and can be used in early planted rice production systems. The objective of this study was to use an association mapping approach to identify candidate genes for cold tolerance at the germination stage. In previous research, over 2000 different global rice accessions were evaluated for their ability to germinate under cold temperatures. The panel included the mini-core (~200 accessions) and the core (~1500 accessions) collections, along with ~400 additional accessions from temperate regions and ~100 breeding/mapping lines. Cleaned seed lots of each accession were surface sterilized and then thirty seeds were evaluated for germination using the ragdoll method with three replicates at 12°C and two replicates at 26°C. Percent germination was determined after one week at 26°C and after one month at 12°C in temperature controlled chambers. Cold germination index was based upon the ratio of germination at 12°C: germination at 26°C. As the study was conducted over a period of three months, repeated checks of the accessions Quilla 66304 (cold tolerant), Lemont (moderate tolerance), and Zhe 733 (cold susceptible) were included as a means of error control. Significant differences were found among the accessions for cold germination tolerance and 590 accessions were equivalent to the cold tolerant check Quilla 66304. Interestingly, these accessions originated from very diverse tropical and temperate growing environments. An association analysis was performed using the mini-core diversity panel genotyped with 154 genome-wide SSRs averaging 10 cM between markers. Results including QTLs associated with cold tolerance at germination and candidate genes will be presented. Subsequent analysis using GBS of the mini-core and accessions in addition to the mini-core panel having superior cold tolerance will be used to validate the initial findings.