Cassava Breeding I: The Value of Breeding Value

Abstract

Breeding cassava relies on several selection stages (single row trial-SRT; preliminary; advanced; and uniform yield trials-UYT). This study uses data from 14 years of evaluations. From more than 20,000 genotypes initially evaluated only 114 reached the last stage. The objective was to assess how the data at SRT could be used to predict the probabilities of genotypes reaching the UYT. Phenotypic data from each genotype at SRT was integrated into the selection index (SIN) used by the cassava breeding program. Average SIN from all the progenies derived from each progenitor was then obtained. Average SIN is an approximation of the breeding value of each progenitor. Data clearly suggested that some genotypes were better progenitors than others (e.g., high number of their progenies reaching the UYT), suggesting important variation in breeding values of progenitors. However, regression of average SIN of each parental genotype on the number of their respective progenies reaching UYT resulted in a negligible coefficient of determination (r (2) = 0.05). Breeding value (e.g., average SIN) at SRT was not efficient predicting which genotypes were more likely to reach the UYT stage. Number of families and progenies derived from a given progenitor were more efficient predicting the probabilities of the progeny from a given parent reaching the UYT stage. Large within-family genetic variation tends to mask the true breeding value of each progenitor. The use of partially inbred progenitors (e.g., S1 or S2 genotypes) would reduce the within-family genetic variation thus making the assessment of breeding value more accurate. Moreover, partial inbreeding of progenitors can improve the breeding value of the original (S0) parental material and sharply accelerate genetic gains. For instance, homozygous S1 genotypes for the dominant resistance to cassava mosaic disease (CMD) could be generated and selected. All gametes from these selected S1 genotypes would carry the desirable allele and 100% of their progenies would be resistant. Only half the gametes produced by the heterozygous S0 progenitor would carry the allele of interest. For other characteristics, progenies from the S1 genotypes should be, at worst, similar to those generated by the S0 progenitors.

Keywords: additive genetic effects; genetic gains; non-additive genetic effects; partial inbreeding; recurrent selection; within-family genetic variation.

Figure 1

Illustration of the different stages of a typical evaluation process in cassava breeding. Plants from germinated seed (seedling plants) are grown in the field and used as the source of clonal planting material (left side). The first evaluation takes place in single row trials (SRT), followed by preliminary (PYT) and advanced (AYT) yield trials. The first multi-location evaluation is in the uniform yield trials (UYT), or sometimes earlier, in the AYTs. Size of plots in UYT has been slightly modified to illustrate the effect of different environments on the growth of cassava.

Figure 2

Relationship between average selection index (SIN) of each progenitor with the respective number of clones representing them at UYT. Extreme average SIN were observed for progenitors represented by fewer than 200 progenies.

Figure 3

Relationship between average selection index (SIN) of each progenitor with the respective number of clones representing them at UYT (arrow identifies SM 1411-5).

Figure 4

Number of families (A) and progenies (B) per progenitor against the number of clones derived from each progenitor reaching UYT (arrow identifies SM 1411-5).

Figure 5

Coefficient of determination for the regression of average SIN at SRT on number of progenies reaching the UYT stage considering different family sizes.

Figure 6

Illustration of the way breeding value could be consistently improved in a stepwise fashion in two “complementary” breeding populations. Squares are used for S₀ genotypes, whereas circles are used for partial inbreds. On the left, selections are made for resistance to CMD. Molecular markers can be used to distinguish homozygous [CC] from heterozygous [Cc] genotypes (❶). In addition to homozygous resistance to CMD, segregating S₁ genotypes are selected for agronomic performance (❷). Diameters of the circles (or size of squares for S₀) in both left and right diagrams represent levels of DMC (larger circles or squares, higher DMC). On the right, selections in the “complementary” population are made for increased dry matter content (❸). This population does not carry resistance to CMD so the genotype for this trait [cc] has not been included in every genotype. The selected products (S₁ genotypes) from these first steps of selection are shaded. Both products, however, are susceptible to a target herbicide. In a parallel process (perhaps from a partner), S₁ genotypes homozygous for a recessive source for tolerance to a herbicide have been generated (❹). The S₁ genotypes selected for resistance to CMD or high DMC are then crossed with the source of tolerance to herbicides. The resulting crosses will be heterozygous for monogenic traits and intermediate for DMC. Self-pollination of the resulting crosses will allow the recovery of S₁ genotypes that are homozygous for CMD and for tolerance to the herbicide (left side), or have improved levels of DMC combined with tolerance to the herbicide (right side). The second-step products are also shaded. Crossing the second-step products generate progenies that are 100% resistant to CMD [Cc], and tolerant to the herbicide [hh] and have excellent levels of DMC.