Association mapping of important agronomic traits in Mucuna pruriens (L.) DC

Abstract

Background: The tropical legume Mucuna pruriens (L.) DC. can meet three agricultural needs: low-cost protein, high-value medicines, and green manure or cover crops. But like other underutilized crops, it needs more modern breeding resources. Identifying marker-trait associations (MTAs) can facilitate marker-assisted breeding and crop improvement. Recent studies have demonstrated the feasibility of identifying MTAs using a small number of accessions (< 100). We have characterized a panel of 70 M. pruriens accessions across two consecutive years and performed association analysis for 16 phenotypic traits related to seed (seed length, seed width, seed thickness, seed yield per plant, hundred seed weight); pod (pod length, pod width, number of pods per cluster, number of pods per plant); inflorescence (inflorescence length, flower buds per inflorescence, flower length, pedicel length), and biochemical attributes (L-DOPA, total protein, total carbohydrate), using 66 genic-microsatellite markers following mixed linear model.

Results: The results showed significant phenotypic (P < 0.05) and genetic diversity (Shannon's information index, I = 0.62) in our germplasm collection. Many tested traits were highly heritable (broad-sense heritability ranging from 42.86 to 99.93%). A total of 15 MTAs was detected at an adjusted significance level of P < 5.55 × 10^{- 3} for nine traits (seed length, seed thickness, seed width, hundred seed weight, seed yield per plant, inflorescence length, flower buds per inflorescence, flower length, and petiole length), contributed by 10 SSR markers (MPU_19, MPU_42, MPU_54, MPU_57, MPU_58, MPU_83, MPU_89, MPU_108, MPU_111, and MPU_122.) with phenotypic variance explained (PVE) ranging from 14.7 to 31.1%. Out of the ten trait-associated markers, the BLAST analysis revealed putative functions of seven markers, except MPU_57, MPU_58, and MPU_83.

Conclusion: Fifteen MTAs identified for important traits with phenotypic variance explained > 10% from mixed linear model offer a solid resource base for improving this crop. This is the first report on association mapping in M. pruriens and our results are expected to assist with marker-assisted breeding and identifying candidate genes in this promising legume.

Keywords: Genetic diversity; Marker-trait association; Population structure; Seed traits.

Fig. 1

Correlation matrix of sixteen phenotypic traits in M. pruriens association mapping panel. Note: The intensity of color ranges from blue (positive) to brown (negative) and the size of the circles show strength of significant correlation (P < 0.05) IL: Inflorescence length; FBpI: Flower buds per inflorescence; FL: Flower length; PedL: Pedicel length; PodL: Pod length; PodW: Pod width; NPpC: Number of pods per cluster; NPpPt: Number of pods per plant; SL: Seed length; SW: Seed width; ST: Seed thickness; SYpPt: Seed yield per plant; HSW: Hundred seed weight; LDp: Total L-DOPA; TPr: Total protein; TCr: Total carbohydrate; ×: Statistically non-significant correlation values

Fig. 2

Scatter plot of M. pruriens accessions based on sixteen phenotypic traits from the principal component analysis (PCA).Note: Red circles, green triangles and blue squares represent M. pruriens var. hirsuta, var. pruriens, and var. utilis, respectively

Fig. 3

Population structure of M. pruriens association mapping panel inferred using STRUCTURE software (a) Hypothetical sub-population estimation using ∆K-values (K = 2) indicating two subpopulations (b) Population structure at K = 2 based on inferred ancestry (Q-matrix) in which two sub-populations are indicated as MpSTR-I (red color) and MpSTR-II (green color)

Fig. 4

Neighbor joining (NJ) dendrogram based on the genetic distance. Note: Red and green color indicates subgroup-1 (MpSTR-I) and subgroup-2 (MpSTR-II) from STRUCTURE analysis

Fig. 5

Scatter plot depicting dispersion of M. pruriens accessions based on principal coordinate analysis. Note: Red and green color indicates subgroup-1 (MpSTR-I) and subgroup-2 (MpSTR-II) from STRUCTURE analysis

Fig. 6

Distribution of global pairwise kinship coefficients (F_ij) of M. pruriens association panel

Fig. 7

Heat map of kinship matrix generated for M. pruriens association mapping panel based on 180 filtered SSR markers data. Dendrogram are shown on the top and left side of the figure

Fig. 8

Manhattan plot (P-value) for MLM depicting significant marker-trait associations at adjusted Bonferroni threshold P < 2.77 × 10^− 4(a) Seed yield per plant (b) Pedicel length; Quantile-Quantile (Q-Q) plot of MLM (c) Seed yield per plant (d) Pedicel length