Abstract
Flooding is a devastating abiotic stress that endangers crop production in the twenty-first century. Because of the severe susceptibility of common bean (Phaseolus vulgaris L.) to flooding, an understanding of the genetic architecture and physiological responses of this crop will set the stage for further improvement. However, challenging phenotyping methods hinder a large-scale genetic study of flooding tolerance in common bean and other economically important crops. A greenhouse phenotyping protocol was developed to evaluate the flooding conditions at early stages. The Middle-American diversity panel (n = 272) of common bean was developed to capture most of the diversity exits in North American germplasm. This panel was evaluated for seven traits under both flooded and non-flooded conditions at two early developmental stages. A subset of contrasting genotypes was further evaluated in the field to assess the relationship between greenhouse and field data under flooding condition. A genome-wide association study using ~150 K SNPs was performed to discover genomic regions associated with multiple physiological responses. The results indicate a significant strong correlation (r > 0.77) between greenhouse and field data, highlighting the reliability of greenhouse phenotyping method. Black and small red beans were the least affected by excess water at germination stage. At the seedling stage, pinto and great northern genotypes were the most tolerant. Root weight reduction due to flooding was greatest in pink and small red cultivars. Flooding reduced the chlorophyll content to the greatest extent in the navy bean cultivars compared with other market classes. Races of Durango/Jalisco and Mesoamerica were separated by both genotypic and phenotypic data indicating the potential effect of eco-geographical variations. Furthermore, several loci were identified that potentially represent the antagonistic pleiotropy. The GWAS analysis revealed peaks at Pv08/1.6 Mb and Pv02/41 Mb that are associated with root weight and germination rate, respectively. These regions are syntenic with two QTL reported in soybean (Glycine max L.) that contribute to flooding tolerance, suggesting a conserved evolutionary pathway involved in flooding tolerance for these related legumes.
Highlights
Low oxygen diffusion in water, prevents its optimal availability to plant organs in flooded conditions and expose plants to hypoxia (e.g., 0% O2 at 20◦C) or anoxia (e.g., 0% O2 at 20◦C)
A phylogenetic tree of the Middle-American Diversity Panel (MDP) was constructed using 6,462 SNPs markers that were in low linkage disequilibrium (LD) (R2 ≤ 0.10)
The pinto and great northern genotypes clustered in one clade representing the Durango/Jalisco race complex, while the majority of black and navy beans grouped in the Mesoamerica cluster
Summary
Low oxygen diffusion in water, prevents its optimal availability to plant organs in flooded conditions and expose plants to hypoxia (e.g., 0% O2 at 20◦C) or anoxia (e.g., 0% O2 at 20◦C). Climate change predictions forecast frequent incidents of flooding that will primarily affect poorlydrained arable farmlands (Bailey-Serres et al, 2012a). This stress will jeopardize food security through yield loss. A drastic decline in diffusion of O2 and CO2 molecules available to the plant from surrounding environments is the most detrimental physiological effect of flooding. This limits ATP synthesis and photosynthesis (BaileySerres and Voesenek, 2008). Excess water causes elevated levels of reactive oxygen species (ROS, Blokhina et al, 2003), cytosol acidification (Fan et al, 1988; Menegus et al, 1991; Felle, 2006), and a decrease in root hydraulic conductivity (Holbrook and Zwieniecki, 2003; Tournaire-Roux et al, 2003)
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