Effectiveness of genomic selection for improving provitamin A carotenoid content and associated traits in cassava

Characterization of grain carotenoids in global sorghum germplasm to guide genomics-assisted breeding strategies

BACKGROUND

Crop biofortification is a successful strategy to ameliorate Vitamin A deficiency. Sorghum is a good candidate for vitamin A biofortification, as it is a staple food in regions with high prevalence of vitamin A deficiency. β-carotene-the main provitamin A carotenoid-is below the target concentration in sorghum grain, therefore biofortification breeding is required. Previous studies found evidence that sorghum carotenoid variation is oligogenic, suggesting that marker-assisted selection can be an appropriate biofortification method. However, we hypothesize that sorghum carotenoids have both oligogenic and polygenic components of variation. Genomics-assisted breeding could accelerate breeding efforts, but there exists knowledge gaps in the genetics underlying carotenoid variation, as well as appropriate germplasm to serve as donors.

RESULTS

In this study, we characterized carotenoids in 446 accessions from the sorghum association panel and carotenoid panel using high-performance liquid chromatography, finding high carotenoid accessions not previously identified. Genome-wide association studies conducted with 345 accessions, confirmed that zeaxanthin epoxidase is a major gene underlying variation for not only zeaxanthin, but also lutein and β-carotene. High carotenoid lines were found to have limited genetic diversity, and originated predominantly from only one country. Potential novel genetic diversity for carotenoid content was identified through genomic predictions in 2,495 accessions of unexplored germplasm. Oligogenic variation of carotenoids was confirmed, as well as evidence for polygenic variation, suggesting both marker-assisted selection and genomic selection can facilitate breeding efforts.

CONCLUSIONS

Sorghum vitamin A biofortification could be beneficial for millions of people who rely on it as a dietary staple. Carotenoid content in sorghum is low, but high heritability suggests that increasing concentrations through breeding is possible. Low genetic diversity among high carotenoid lines might be the main limitation for breeding efforts, therefore further germplasm characterization is needed to assess the feasibility of biofortification breeding. Based on germplasm here evaluated, most countries' germplasm lacks high carotenoid alleles, thus pre-breeding will be needed. A SNP marker within the zeaxanthin epoxidase gene was identified as a good candidate for use in marker-assisted selection. Due to the oligogenic and polygenic variation of sorghum grain carotenoids, both marker-assisted selection and genomic selection can be employed to accelerate breeding efforts.

Validation of KASP markers associated with cassava mosaic disease resistance, storage root dry matter and provitamin A carotenoid contents in Ugandan cassava germplasm

INTRODUCTION

The intrinsic high heterozygosity of cassava makes conventional breeding ineffective for rapid genetic improvement. However, recent advances in next generation sequencing technologies have enabled the use of high-density markers for genome-wide association studies, aimed at identifying single nucleotide polymorphisms (SNPs) linked to major traits such as cassava mosaic disease (CMD) resistance, dry matter content (DMC) and total carotenoids content (TCC). A number of these trait-linked SNPs have been converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers for downstream application of marker assisted selection.

METHODS

We assayed 13 KASP markers to evaluate their effectiveness in selecting for CMD, DMC and TCC in 1,677 diverse cassava genotypes representing two independent breeding populations in Uganda.

RESULTS

Five KASP markers had significant co-segregation with phenotypes; CMD resistance (2), DMC (1) and TCC (2), with each marker accounting for at least 30% of the phenotypic variation. Markers located within the chromosomal regions for which strong marker-trait association loci have been characterised (chromosome 12 markers for CMD, chromosome 1 markers for DMC and TCC) had consistently superior ability to discriminate the respective phenotypes.

DISCUSSION

The results indicate varying discriminatory abilities of the KASP markers assayed and the need for their context-based use for MAS, with PSY2_572 particularly effective in selecting for high TCC. Availing the effective KASP markers on cost-effective genotyping platforms could facilitate practical implementation of marker-assisted cassava breeding for accelerated genetic gains for CMD, DMC and provitamin A carotenoids.

Phenotypic diversity and selection in biofortified cassava germplasm for yield and quality root traits

Increasing carotenoid content and improving other root quality traits has been the focus of cassava biofortification. This study aimed to (i) evaluate the genetic variability for total carotenoid content (TCC), as well as for root yield and root quality attributes; (ii) estimate potentially useful correlations for selection; and (iii) select parents for breeding and estimate the genetic gain. Data from 2011 to 2020 of 265 cassava genotypes with cream and yellow roots were analyzed for dry matter content (DMC), shoot yield, fresh root yield (FRY), dry root yield (DRY), harvest index, average number of roots per plant, starch content, root pulp color, cyanogenic compounds, and TCC. The best linear unbiased predictions showed great phenotypic variation for all traits. Six distinct groups were formed for productive characteristics of root quality, mainly TCC, DMC and FRY. Only TCC showed high broad-sense heritability ( h 2 = 0.72), while the other traits had low to medium magnitude (0.21 ≤ h 2 ≤ 0.60). TCC was strongly correlated with pulp color (r = 0.70), but null significance for DMC. The network analysis identified a clear separation between the agronomic and quality attributes of cassava roots. The selection of the 30 genotypes for recombination in the breeding program has the potential to raise TCC by 27.05% and reduce the cyanogenic compounds content by 23.03%, in addition to increasing FRY and DRY by 22.72% and 22.95%, respectively. This is the first consolidated study on the potential of germplasm for the development biofortified cassava cultivars in Brazil.

Advances in integrated genomic selection for rapid genetic gain in crop improvement: a review

Genomic selection and its importance in crop breeding. Integration of GS with new breeding tools and developing SOP for GS to achieve maximum genetic gain with low cost and time. The success of conventional breeding approaches is not sufficient to meet the demand of a growing population for nutritious food and other plant-based products. Whereas, marker assisted selection (MAS) is not efficient in capturing all the favorable alleles responsible for economic traits in the process of crop improvement. Genomic selection (GS) developed in livestock breeding and then adapted to plant breeding promised to overcome the drawbacks of MAS and significantly improve complicated traits controlled by gene/QTL with small effects. Large-scale deployment of GS in important crops, as well as simulation studies in a variety of contexts, addressed G × E interaction effects and non-additive effects, as well as lowering breeding costs and time. The current study provides a complete overview of genomic selection, its process, and importance in modern plant breeding, along with insights into its application. GS has been implemented in the improvement of complex traits including tolerance to biotic and abiotic stresses. Furthermore, this review hypothesises that using GS in conjunction with other crop improvement platforms accelerates the breeding process to increase genetic gain. The objective of this review is to highlight the development of an appropriate GS model, the global open source network for GS, and trans-disciplinary approaches for effective accelerated crop improvement. The current study focused on the application of data science, including machine learning and deep learning tools, to enhance the accuracy of prediction models. Present study emphasizes on developing plant breeding strategies centered on GS combined with routine conventional breeding principles by developing GS-SOP to achieve enhanced genetic gain.

Agogbua J, R. Keyagha E, I. Nkanga I. Carotenoids in Cassava (Manihot esculenta Crantz)

Cassava is produced globally and consumed as an important staple in Africa for its calories, but the crop is deficient in micronutrients such as vitamin A. Pro-vitamin A carotenoids including β-carotene are precursors of vitamin A in the human body. Carotenoids are generally associated with colors of fruits and vegetables. Although most cassava varieties have white tuberous roots and generally accepted, naturally; some cassava roots are colored yellow and contain negligible amounts of vitamin A. Several genes have been identified in the carotenoids biosynthesis pathway of plants, but studies show that Phytoene synthase 2 (PSY2), lycopene epsilon cyclase, and β-carotene hydroxylase genes have higher expression levels in yellow cassava roots. So far, the PSY2 gene has been identified as the key gene associated with carotenoids in cassava. Some initiatives are implementing conventional breeding to increase pro-vitamin A carotenoids in cassava roots, and much success has been achieved in this regard. This chapter highlights various prediction tools employed for carotenoid content in fresh cassava roots, including molecular marker-assisted strategies developed to fast-track the conventional breeding for increased carotenoids in cassava.