Marker-based linkage map of Andean common bean (Phaseolus vulgaris L.) and mapping of QTLs underlying popping ability traits

Abstract

Background: Nuña bean is a type of ancient common bean (Phaseolus vulgaris L.) native to the Andean region of South America, whose seeds possess the unusual property of popping. The nutritional features of popped seeds make them a healthy low fat and high protein snack. However, flowering of nuña bean only takes place under short-day photoperiod conditions, which means a difficulty to extend production to areas where such conditions do not prevail. Therefore, breeding programs of adaptation traits will facilitate the diversification of the bean crops and the development of new varieties with enhanced healthy properties. Although the popping trait has been profusely studied in maize (popcorn), little is known about the biology and genetic basis of the popping ability in common bean. To obtain insights into the genetics of popping ability related traits of nuña bean, a comprehensive quantitative trait loci (QTL) analysis was performed to detect single-locus and epistatic QTLs responsible for the phenotypic variance observed in these traits.

Results: A mapping population of 185 recombinant inbred lines (RILs) derived from a cross between two Andean common bean genotypes was evaluated for three popping related traits, popping dimension index (PDI), expansion coefficient (EC), and percentage of unpopped seeds (PUS), in five different environmental conditions. The genetic map constructed included 193 loci across 12 linkage groups (LGs), covering a genetic distance of 822.1 cM, with an average of 4.3 cM per marker. Individual and multi-environment QTL analyses detected a total of nineteen single-locus QTLs, highlighting among them the co-localized QTLs for the three popping ability traits placed on LGs 3, 5, 6, and 7, which together explained 24.9, 14.5, and 25.3% of the phenotypic variance for PDI, EC, and PUS, respectively. Interestingly, epistatic interactions among QTLs have been detected, which could have a key role in the genetic control of popping.

Conclusions: The QTLs here reported constitute useful tools for marker assisted selection breeding programs aimed at improving nuña bean cultivars, as well as for extending our knowledge of the genetic determinants and genotype x environment interaction involved in the popping ability traits of this bean crop.

Figure 1

Genetic linkage map of common bean based on the RIL population PMB0225 x PHA1037. Location of single-locus QTLs and E-QTLs controlling popping traits: popping dimension index (PDI), expansion coefficient (EC), and percentage of unpopped seeds (PUS). Common SSR markers to previously published maps (see text for references) are indicated in bold. Names of QTLs are listed in Tables 5, 6, and 7. Cumulative distances among markers are indicated in cM to the left of the linkage group, names of markers are shown on the right. QTLs are depicted as vertical bars to the right of the linkage groups. QTLs detected by both MapQTL and QTLNetwork software packages are indicated in black, QTLs identified only by MapQTL are shown in red, and QTLs detected only by QTLNetwork are represented in blue. Epistatic interactions between QTLs are represented with numbered stars.

Figure 2

Unpopped and popped seeds of the parental genotypes. Both PMB0225 (A) and PHA1037 (B) belong to the Andean gene pool of common bean. Scale bar 1 cm.