Review

Germplasm-regression-combined marker-trait association identification in plants

Chengjiang Ruan

Dalian Nationalities University, Institute of Bio-Resources and Environment, No.18 Liaohe Western Road or Dalian Economic and Technical Development Zone, Dalian City, Liaoning Province 116600, P.R. China.

E-mail: ruancj@yahoo.com.cn.  Fax: +86-411-87618179.

Abbreviations: QTL, quantitative trait loci; MAS, marker assisted selection; GRC, germplasm-regression-combined; RAPD, random amplified polymorphic DNA; RFLP, restriction fragment length polymorphism; AFLP, amplified fragment length polymorphism; ISSR, inter-simple sequence repeats; SAMPL, selective amplification of microsatellite polymorphic loci; SSR, simple sequence repeat; SCAR, sequence characterized amplified region; SNP, single nucleotide polymorphism; PCR, polymerase chain reaction.

Accepted 31 December, 2009

   Abstract

In the past 20 years, the major effort in plant breeding has changed from quantitative to molecular genetics with emphasis on quantitative trait loci (QTL) identification and marker assisted selection (MAS). However, results have been modest. This has been due to several factors including absence of tight linkage QTL, non-availability of mapping populations and lack of substantial time needed to develop such populations. To overcome these limitations and as an alternative to planned populations, molecular marker- trait associations have been identified by the combination between germplasm and the regression technique. In the present preview, we first surveyed the successful applications of germplasm-regression-combined (GRC) molecular marker-trait association identification in plants; secondly, we described how to do the GRC analysis and its differences from mapping QTL based on a linkage map reconstructed from the planned populations; thirdly, we considered the factors that affect the GRC association identification, including selections of optimal germplasm and molecular markers and testing of identification efficiency of markers associated with traits; and finally we discussed the future prospects of GRC marker-trait association analysis used in plant MAS/QTL breeding programs, especially in long-juvenile woody plants when no other genetic information such as linkage maps and Quantitative Trait Loci are available.

Key words: Association analysis, marker assisted selection (MAS), molecular marker, quantitative trait, germplasm-regression.