Genome-Wide Association Studies on Resistance to Pea Weevil: Identification of Novel Sources of Resistance and Associated Markers

Abstract

Little resistance to the pea weevil insect pest (Bruchus pisorum) is available in pea (Pisum sativum) cultivars, highlighting the need to search for sources of resistance in Pisum germplasm and to decipher the genetic basis of resistance. To address this need, we screened the response to pea weevil in a Pisum germplasm collection (324 accession, previously genotyped) under field conditions over four environments. Significant variation for weevil seed infestation (SI) was identified, with resistance being frequent in P. fulvum, followed by P. sativum ssp. elatius, P. abyssinicum, and P. sativum ssp. humile. SI tended to be higher in accessions with lighter seed color. SI was also affected by environmental factors, being favored by high humidity during flowering and hampered by warm winter temperatures and high evapotranspiration during and after flowering. Merging the phenotypic and genotypic data allowed genome-wide association studies (GWAS) yielding 73 markers significantly associated with SI. Through the GWAS models, 23 candidate genes were found associated with weevil resistance, highlighting the interest of five genes located on chromosome 6. These included gene 127136761 encoding squalene epoxidase; gene 127091639 encoding a transcription factor MYB SRM1; gene 127097033 encoding a 60S ribosomal protein L14; gene 127092211, encoding a BolA-like family protein, which, interestingly, was located within QTL BpLD.I, earlier described as conferring resistance to weevil in pea; and gene 127096593 encoding a methyltransferase. These associated genes offer valuable potential for developing pea varieties resistant to Bruchus spp. and efficient utilization of genomic resources through marker-assisted selection (MAS).

Keywords: Bruchus; GWAS; Pisum; resistance breeding.

Figure 1

Histogram distribution and SI correlation between environments. *** indicate statistically significant correlation at 0.05, 0.01 and 0.001 level respectively.

Figure 2

Boxplot representing the SIr (Seed Infestation relative to the control cv. Messire, established at 100%) value in each environment categorized by material type, flower color, taxa, and seed color. Red dashed lines show the average SI value of each environment. The most resistant group in each category with a p-value < 0.001 is highlighted in teal color.

Figure 3

Genotype plus genotype–environment interaction biplot.

Figure 4

Boxplot representing the influence of maturity stage on seed infestation (SIr). Red dashed lines represent the average SIr by environment.

Figure 5

NMDS analysis. The biplot shows the climatic variables that participate in the SI variation by environment with a p < 0.05. These climatic variables are grouped in two clusters: (i) at the left, maximum temperature at pre-flowering (Pre_Tmax), accumulated evapotranspiration until flowering (Flow_Eto), and accumulated evapotranspiration post flowering (Post_Eto) and (ii) average humidity and maximum humidity until flowering (Flow_Have and Flow_Hmax, respectively).

Figure 6

Q-Q (a) and Manhattan (b) plots of the BLINK model output. Blue dashed lines represent three genomic regions where combination of same MTAs in different environments occurred.

Figure 7

Phenotypic response of each allelic variation by environment of the marker DArT_3542707 located in the gene Psat6g101920 of the Cameor genome, corresponding with gene 127092211 (NCBI gene ID) in ZW6 genome. * and ** represent significant pair-wise differences in the level of SI between allelic variant at 0.05 and 0.01 respectively.