Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.)

Abstract

We have identified QTLs for stomatal characteristics on chromosome II of faba bean by applying SNPs derived from M. truncatula , and have identified candidate genes within these QTLs using synteny between the two species. Faba bean (Vicia faba L.) is a valuable food and feed crop worldwide, but drought often limits its production, and its genome is large and poorly mapped. No information is available on the effects of genomic regions and genes on drought adaptation characters such as stomatal characteristics in this species, but the synteny between the sequenced model legume, Medicago truncatula, and faba bean can be used to identify candidate genes. A mapping population of 211 F5 recombinant inbred lines (Mélodie/2 × ILB 938/2) were phenotyped to identify quantitative trait loci (QTL) affecting stomatal morphology and function, along with seed weight, under well-watered conditions in a climate-controlled glasshouse in 2013 and 2014. Canopy temperature (CT) was evaluated in 2013 under water-deficit (CTd). In total, 188 polymorphic single nucleotide polymorphisms (SNPs), developed from M. truncatula genome data, were assigned to nine linkage groups that covered ~928 cM of the faba bean genome with an average inter-marker distance of 5.8 cM. 15 putative QTLs were detected, of which eight (affecting stomatal density, length and conductance and CT) co-located on chromosome II, in the vicinity of a possible candidate gene-a receptor-like protein kinase found in the syntenic interval of M. truncatula chromosome IV. A ribose-phosphate pyrophosphokinase from M. truncatula chromosome V, postulated as a possible candidate gene for the QTL for CTd, was found some distance away in the same chromosome. These results demonstrate that genomic information from M. truncatula can successfully be translated to the faba bean genome.

QTL detection for flowering time in faba bean and the responses to ambient temperature and photoperiod

“…Faba bean has a high level of macrosynteny with these legumes (Rispail et al 2010;Cruz-Izquierdo et al 2012;Kaur et al 2014;Khazaei et al 2014), so this synteny could be used to extend knowledge to faba bean, help to compare genomic regions across different populations that use different markers and even help identify candidate genes underlying flowering QTLs detected in faba bean.…”

Genetic Linkage Maps and Homology Study of Backcross Families of German Faba Bean (Vicia fabaL.)

“…This marker was 32.8 cM distant from common marker E32M58-243 C with four markers in-between. That common marker was located at position 175.3 cM in LG05 in the M-set (Khazaei et al 2014;Welna 2014) and corresponded with LG03 of another consensus map (Cottage et al 2012;Donal O'Sullivan, University of Reading, UK, personal communication). This was based on 13 common SNP marker positions between M-set and the consensus map provided by Donal O'Sullivan.…”

“…Linkage maps were utilized to locate quantitative trait loci (QTL) associated with resistance to biotic stresses (Ávila et al 2003, 2004), as well as markers tightly linked to abiotic stresses tolerance (Arbaoui et al 2008;Khazaei et al 2014;Salam 2014;Welna 2014). Furthermore, QTL linked to nutritional value of seeds (Gutiérrez et al 2007(Gutiérrez et al , 2008, and growth habit (Ávila et al 2006, 2007) have been detected.…”

Exploiting Germplasm Resources for Climate-Change Adaptation in Faba Bean

“…In the progeny, QTLs for stomatal density, stomatal length, and both stomatal conductance and canopy temperature in well-watered conditions, co-located on chromosome II, with increased conductance and cooler leaves associated with the Mélodie allele. At the other end of the same chromosome, about 130 cm away, was another locus affecting canopy temperature in water-deficit conditions, where the allele conferring cooler leaves came from ILB938 (Khazaei et al 2014b). We now have the possibility to test the four possible combinations of these alleles for their effects on water use in well-watered and water-limited conditions, in an otherwise random genetic background, and determine whether there is an advantage conferred by any particular combination.…”

“…The F 5 generation of Mélodie/2 × ILB938/2, comprising 211 recombinant inbred lines, was subjected to SNP genotyping at 188 loci and was phenotyped in the glasshouse (Khazaei et al 2014b). The stomatal conductance of Mélodie was much greater than that of ILB938 in well-watered conditions, but dropped below that of ILB938 when soil moisture was reduced to one-tenth of field capacity.…”