Quantitative Trait Locus Analysis of Growth-Related Traits in a New Arabidopsis Recombinant Inbred Population

Abstract

Arabidopsis natural variation was used to analyze the genetics of plant growth rate. Screening of 22 accessions revealed a large variation for seed weight, plant dry weight and relative growth rate but not for water content. A positive correlation was observed between seed weight and plant area 10 d after planting, suggesting that seed weight affects plant growth during early phases of development. During later stages of plant growth this correlation was not significant, indicating that other factors determine growth rate during this phase. Quantitative trait locus (QTL) analysis, using 114 (F9 generation) recombinant inbred lines derived from the cross between Landsberg erecta (Ler, from Poland) and Shakdara (Sha, from Tadjikistan), revealed QTLs for seed weight, plant area, dry weight, relative growth rate, chlorophyll fluorescence, flowering time, and flowering-related traits. Growth traits (plant area, dry weight, and relative growth rate) colocated at five genomic regions. At the bottom of chromosome 5, colocation was found of QTLs for leaf area, leaf initiation speed, specific leaf area, and chlorophyll fluorescence but not for dry weight, indicating that this locus might be involved in leaf development. No consistent relation between growth traits and flowering time was observed despite some colocations. Some of the QTLs detected for flowering time overlapped with loci detected in other recombinant inbred line populations, but also new loci were identified. This study shows that Arabidopsis can successfully be used to study the genetic basis of complex traits like plant growth rate.

New Arabidopsis Recombinant Inbred Line Populations Genotyped Using SNPWave and Their Use for Mapping Flowering-Time Quantitative Trait Loci

“…In addition, we included the accession Shakdara (Sha) that is assumed to contain a weak FLC allele (Gazzani et al 2003;Michaels et al 2003). This is in agreement with the absence of a late-flowering Sha allele at the FLC locus in populations made from crosses with Sha (Loudet et al 2002;El-Lithy et al 2004). …”

“…Kas-2 and Kond have late alleles at the FRI locus, which is at least functional in Kond (Gazzani et al 2003;Michaels et al 2003;Hagenblad et al 2004). Active FRI alleles may confer lateness without FLC, as was also found in Sha-derived populations (Loudet et al 2002;El-Lithy et al 2004). In the Ler 3 An-1 population, a novel locus was also identified at the top of chromosome 4, for which An-1 accelerates FT.…”

“…QTL mapping of flowering time: Flowering-time QTL have been mapped in several Arabidopsis RIL populations (Kowalski et al 1994;Clarke et al 1995;Jansen et al 1995;Kuittinen et al 1997;Alonso-Blanco et al 1998a;Loudet et al 2002;El-Lithy et al 2004;Koornneef et al 2004 for review). Since different populations may segregate for different loci depending on the genetic composition of their parental lines, a comparison between multiple crosses is needed to obtain information about the variation present among Arabidopsis accessions.…”

“…At these positions also the Sha accession from Tadjikistan carries similar alleles (Loudet El-Lithy et al 2004). Kas-2 and Sha may have similar alleles for the QTL at the bottom of chromosome 1 for which the FLM locus is a candidate gene (Werner et al 2005).…”

Natural Diversity in Flowering Responses of Arabidopsis thaliana Caused by Variation in a Tandem Gene Array

“…Segregation distortion at MAF2: Several studies have reported a flowering-time QTL in the vicinity of the MAF locus, as well as a segregation distortion favoring the early flowering allele (Loudet et al 2002;El-Lithy et al 2004Simon et al 2008). To determine the frequency of the insertion alleles relative to MAF2-Ler, we analyzed the BC 5 F 2 segregating populations.…”