Ismail Y. Rabbi
In December 2020, the IITA Cassava Breeding Program and the National Root Crops Research Institute (NRCRI) released four NextGen cassava varieties in Nigeria under the Next Generation Cassava Breeding
Project (www.nextgencassava.org). This achievement is the culmination of an ambitious modernization program and demonstrates the first products of molecular breeding and genomic selection breeding in cassava
globally.
The released varieties address the increasing demands from farmers and processors for more productive clones with higher starch content and multiple-stress tolerance. The modernization efforts include mainstreaming predictive breeding through genomic selection, complete digitization of phenotype data collection, and better control of flowering.
Genomic resources developed
Until recently, cassava was classified as an orphan crop with inadequate access to modern breeding technologies, particularly genomic resources for genetic studies and predictive breeding, despite the crop’s
significant role in ensuring food security for more than half a billion people in the tropics. Breeders traditionally rely on recurrent phenotypic selection, and it takes several years to complete a breeding cycle. This lengthy population cycling time is due to the crop’s long maturity period of at least 12 months, low clonal multiplication rate, and limited seed set per cross.
As a result of the low multiplication rate, several propagation cycles are needed to obtain sufficient material for replicated and multilocational evaluation. Consequently, it typically takes five to six years from seedling germination to multilocation yield trials. In addition, cassava genotypes show wide variation in flowering time, rate, and fertility, limiting the number of successful crosses a breeder can make between selected parental clones.
To address these challenges, scientists at IITA, collaborating with national and international partners, embarked on a journey to modernize cassava breeding. The first achievement was developing sufficient genomic resources for the crop, including chromosome-scale reference genome and a detailed haplotype map from re-sequencing important landraces, elite breeding lines, and wild cassava diverse accessions (Ramu et al. 2017).
A catalog of genes controlling important traits in cassava
Concurrent with the generation of genomic resources, the team at IITA led global efforts to pinpoint the genomic regions that control the variation of key traits in African cassava germplasm. A detailed catalog of more than 40 chromosomal regions or SNP markers associated with 14 desirable traits related to biotic stress, root quality, and agro-morphology was published (Rabbi et al. 2020). This output resulted from a large genome-wide association study involving more than 5,130 clones developed in Nigeria at the IITA Cassava Breeding Program that were genotyped at high density and phenotyped at several locations over four years.
It is well known that trait-linked marker discovery does not automatically translate to deployment in breeding programs. One of the reasons for the slow uptake is a failure to translate genomic knowledge into assays/tools that breeders can easily use to support selection decisions. To overcome this bottleneck, the discovery team converted the markers anchoring the genes of several traits into a set of robust assays that are available marker-assisted selection (MAS) to any cassava breeder worldwide through independent genotyping service providers. The initial traits include resistance to cassava mosaic disease—a major biotic constraint to the crop’s productivity, increased provitamin A content for biofortification, and increased dry matter content.
For the first time, these assays have been deployed to overcome new outbreaks of cassava mosaic disease in Southeast Asia, particularly Vietnam, Thailand, and China (Ige et al. 2021). IITA shipped varieties with inbuilt resistance to the disease and the markers linked to the resistance genes to breeders in Asia. This has permitted rapid mobilization of the resistance genes into locally adapted cassava varieties in Asia.
The benefits of overcoming cassava mosaic disease are immense. In Africa, the disease causes yield losses of up to 80% depending on infection type and cassava variety. These translate into an annual reduction of more than 30 million tons of fresh root yield. The thriving Asian cassava industry is also at risk of severe disease that would result in huge losses if not addressed in time.
Another significant milestone in molecular breeding progress at IITA is the addition of a new set of markers associated with low cyanogenic potential into the breeders’ toolbox. Together with scientists from the Brazilian Agricultural Research Corporation (EMBRAPA) and Boyce Thompson Institute in Cornell University, scientists from IITA discovered major genes associated with the accumulation of the toxic compounds in cassava roots (Ogbonna et al. 2020). Cyanide glucosides are toxic metabolic products found in varying concentrations in different cassava genotypes. Varieties with high concentrations of these compounds must be processed thoroughly before consumption. Breeding for low cyanogenic potential is rather cumbersome due to the technical complexity associated with the measurement of the compound. Availability of markers linked to low cyanide content genes is now helping to make selections easier and cheaper, allowing breeders to screen thousands of lines at early breeding stages.
Genomic selection: From proof-of-concept to products
Another innovation in cassava breeding is genomic selection to predict breeding values and clone performance at the seedling stage before field testing. This approach, initially pioneered in animal breeding, is useful for complex traits such as yield and yield components that are controlled by a large number of genes with small effects. Genomic selection works through statistical modeling of marker and phenotype data in a training population and then using the developed models to predict phenotypes in new lines that have only been genotyped.
The IITA breeding program has shortened the breeding cycle from at least five years to two years using genomic selection. The program has been able to carry out five cycles of population improvement since 2012, culminating in the release of the four varieties in 2020. These include IITA-TMS-IBA000070 (Baba 70), IITA-TMS13F1343P0022 (Obasanjo 2), IITA-TMS13F1160P0004 (Game Changer), and NR130124 (Hope, developed by NRCRI). They are characterized by high yield, high dry matter content, resistance to cassava mosaic disease, and wide adaptation.
To facilitate the mainstreaming of molecular breeding, the NextGen Cassava Project has developed CassavaBase, an open-access breeding database (https://cassavabase.org). The user-friendly database is critical for the efficient management of large amounts of genotype and phenotype data. Breeders from around the world currently use the database to (1) track breeding accessions; (2) design field trials; (3) store field trial data; (4) capture phenotype data using standardized ontologies; (5) store genotypic data, including from Next Generation Sequencing platforms; and (6) implement standard algorithms for breeding trial analysis and selection decisions.
Certainly, cassava has come a long way from being an orphan crop following the significant advances in the modernization of breeding approaches as outlined above. Still, much remains to be done, particularly for mainstreaming molecular breeding approaches in national breeding programs across Africa.
Funding
The Bill & Melinda Gates Foundation (Grant INV—007637 http://www.gatesfoundation.org); the UK Foreign, Commonwealth and Development Office (FCDO); and the Roots, Tubers and Bananas Program of CGIAR.
Partners
- International Institute of Tropical Agriculture (Nigeria)
- National Root Crops Research Institute (Nigeria)
- National Crops Resources Research Institute (Uganda)
- Tanzania Agricultural Research Institute
- Brazilian Agricultural Research Corporation (Brazil)
- International Center for Tropical Agriculture (Colombia)
- Cornell University (New York)
- Boyce Thompson Institute (New York)
- USDA-ARS (Ithaca, New York; Hilo, Hawaii)