Genomics-Assisted Breeding in the CGIAR Research Program on Roots, Tubers and Bananas (RTB)

Abstract

Breeding in the CGIAR Research Program on Roots, Tubers and Bananas (RTB) targets highly diverse biotic and abiotic constraints, whilst meeting complex end-user quality preferences to improve livelihoods of beneficiaries in developing countries. Achieving breeding targets and increasing the rate of genetic gains for these vegetatively propagated crops, with long breeding cycles, and genomes with high heterozygosity and different ploidy levels, is challenging. Cheaper sequencing opens possibilities to apply genomics tools for complex traits, such as yield, climate resilience, and quality traits. Therefore, across the RTB program, genomic resources and approaches, including sequenced draft genomes, SNP discovery, quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS), are at different stages of development and implementation. For some crops, marker-assisted selection (MAS) is being implemented, and GS has passed the proof-of-concept stage. Depending on the traits being selected for using prediction models, breeding schemes will most likely have to incorporate both GS and phenotyping for other traits into the workflows leading to varietal development.

Prioritising quality traits for gender‐responsive breeding for boiled potato in Uganda

“…Potato breeding has focused on increasing yields and disease tolerance, while other traits preferred by men and women farmers and markets are given a low priority. Friedmann et al, (2018), suggest that it is important to understand any gender differences in trait preferences because breeding programmes that do not take these differences into account may exacerbate gender inequalities and result in negative outcomes for women. Tufan et al, (2018) note that there is lack of information and tools to understand gender differences in trait preferences an understanding of these gender differences should influence breeding decisions1.…”

Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops

“…In recent years many large‐scale efforts have sought to further understand these crops using genome sequences (Xu et al , ; D'Hont et al , ; Wang et al , ; Tamiru et al , ; Yang et al , ; Li et al , ) and genome diversity studies (Bredeson et al , ; Hardigan et al , ; Nyine et al , ; Christelová et al , ; Muñoz‐Rodríguez et al , ; Němečková et al , ), genetic selection (Wolfe et al , ), molecular markers (QTLs) (Monden and Tahara, ; Kim et al , ; Sharma and Bryan, ), and comparative transcriptome resources (Kundapura Venkataramana et al , ; Sarah et al , ; van Wesemael et al , ; Cenci et al , ) widely developed alongside morphologic, agronomic and phenotypic classifications (Oliveira et al , ; Rahajeng and Rahayuningsih, ; Dépigny et al , ; Girma et al , ; van Wesemael et al , ). The progress of the CGIAR Research Program on Roots, Tubers and Bananas (http://www.rtb.cgiar.org), applying genomics‐assisted breeding to RTBs, has recently been reviewed (Friedmann et al , ). Although typically in the early stages, the authors noted that success will be dependent upon the quality of phenotypic characterization.…”

Selecting for useful properties of plants and fungi – Novel approaches, opportunities, and challenges

“…In the staple food crop cassava, in which phenotypic selection alone is inefficient and heritability of desired traits is low, genomic selection has been shown to accurately predict yield traits in multiple trials (de Andrade, Sousa, Oliveira, Resende, & Azevedo, 2019). Nevertheless, the presence of polyploidy and high heterozygosity in many crop genomes is currently limiting the widespread application of genomic selection (Friedmann et al., 2018).…”