Genetic parameters, prediction, and selection in a white Guinea yam early-generation breeding population using pedigree information

Abstract

Better understanding of the genetic control of traits in breeding populations is crucial for the selection of superior varieties and parents. This study aimed to assess genetic parameters and breeding values for six essential traits in a white Guinea yam (Dioscorea rotundata Poir.) breeding population. For this, pedigree-based best linear unbiased prediction (P-BLUP) was used. The results revealed significant nonadditive genetic variances and medium to high (.45-.79) broad-sense heritability estimates for the traits studied. The pattern of associations among the genetic values of the traits suggests that selection based on a multiple-trait selection index has potential for identifying superior breeding lines. Parental breeding values predicted using progeny performance identified 13 clones with high genetic potential for simultaneous improvement of the measured traits in the yam breeding program. Subsets of progeny were identified for intermating or further variety testing based on additive genetic and total genetic values. Selection of the top 5% progenies based on the multi-trait index revealed positive genetic gains for fresh tuber yield (t ha^-1), tuber yield (kg plant^-1), and average tuber weight (kg). However, genetic gain was negative for tuber dry matter content and Yam mosaic virus resistance in comparison with standard varieties. Our results show the relevance of P-BLUP for the selection of superior parental clones and progenies with higher breeding values for interbreeding and higher genotypic value for variety development in yam.

FIGURE 1

Clustering of the 1,420 yam breeding lines with discriminant analysis (DA) of principal components on pedigree‐based relationship matrix. PCA, principal component analysis

FIGURE 2

Genetic variance partitioning of six white Guinea yam traits in 1,420 early‐generation breeding lines for the genetic models accounting for different covariance structures from a pedigree relationship. A, additive model. A+D, additive plus dominance model; YMV, Yam mosaic virus; AUDPC, area under the disease progress curve

FIGURE 3

Variation in heritability estimates (broad sense and narrow sense) with three different models for the six traits in white Guinea yam. A, genetic model with additive covariance structure from the pedigree matrix; A+D, genetic model with additive plus dominance covariance structure from the pedigree matrix; B, baseline model with independent clone effect. H ² is broad‐sense heritability. h ² is narrow‐sense heritability

FIGURE 4

The pattern of genetic correlations among the six white Guinea yam traits. Statistical significance is labeled ^* p < .05, ^** p < .01, ^*** p < .001. TTY, fresh tuber yield (t ha⁻¹); TTWPL, fresh tuber yield per plant (kg); ATW, average tuber weight (kg tuber⁻¹); TTNPL, tuber number per plant (count); DM, tuber dry matter content (%); YMV, Yam mosaic virus severity score (area under the disease progress curve [AUDPC] value)

FIGURE 5

Distribution of the parental clones and their progenies based on the breeding and genotypic values estimated through the restricted maximum likelihood (REML) procedure involving pedigree information. (a) Parental clone ranking on net genetic worth for the multiple trait selection indices for breeding value estimates based on progeny performance, (b) distributions of the clonal progenies for selection index on net breeding and genotypic values for multiple traits. The graph in Panel b presents individual progeny genotypes as blue dots. The red and black dotted lines represent the cut‐point for selection index at 5% intensity

FIGURE 6

Comparison of realized and expected genetic gains for measured traits with multi‐trait index and single‐trait selection strategies. YMV, Yam mosaic virus severity (area under the disease progress curve [AUDPC] value); TTNL, tubers per plant (count); TTWPL, fresh tuber yield per plant (kg); TTY, fresh tuber yield (t ha⁻¹); ATW, average tuber weight (kg); DM, tuber dry matter content (%)