Genomic tools for exploiting germplasm resources to improve grain attributes in sorghum: A case of Ethiopian sorghum germplasm collection

Date

2023-05-01

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Abstract

Sorghum is a primary source of diet for millions of people living in the semi-arid regions of Sub-Saharan Africa and Asia. Due to its immense resilience, sorghum stands as the crop of choice in the face of climate change that has already been causing widespread crop failures. However, the low nutritional quality of sorghum has negatively impacted its use and marketability relative to other cereals. Given the vast untapped germplasm resources for the species, opportunities exist to exploit beneficial alleles that may be of value to tackle challenges related to sorghum production and utilization. The current work is focused on exploring germplasm resources from one of the most significant sources of diversity, Ethiopia, to lay the scientific basis for genetic improvement of sorghum nutritional traits with emphasis on protein and the role of grain physicochemical attributes on adaptation behavior of the species. The work is presented in four chapters. The first chapter deals with a review of background information on the nutritional attributes of cereals emphasizing on challenges and opportunities for improving protein content; the second part investigates the pattern of adaptation of sorghum across Ethiopia’s diverse agroecology in view of bioclimatic factors vis-a-vis grain physicochemical attributes and genomic profile; the third chapter explores the power of genomics for mining germplasm resources in gene banks; the last chapter focuses on the impact of grain pre-treatment on bio-availability of proteins from a fermented sorghum food product. In the second chapter, after the background review, the hypothesis that environmental factors shape sorghum grain attributes was tested using more than 1500 Ethiopian landraces. We utilized phenotype-environment and genome-environment associations to support the thesis. The phenotype-environment association supports the hypothesis that tannin presence, grain weight, kernel hardness, and panicle compactness are all associated with historic precipitation gradient. The correlation pattern revealed by principal component analysis fits the expectation that grain attributes that favor grain-related diseases, such as compact panicles, were mainly concentrated in drier areas. In contrast, traits like tannin presence and loose panicle dominate high precipitation areas. Moreover, landraces from low rainfall regions were susceptible to grain mold suggesting the need to incorporate resistance when materials from dry regions are used as breeding parent for developing varieties for high precipitation areas. Genome-environment association also revealed the importance of polyphenols for the adaptation of sorghum. Moreover, the genomic loci attributed to historical population structure were correlated with precipitation and temperature gradients. The study suggests that sorghum improvement endeavors targeting grain attributes should also consider the climatic condition of the target environments. Likewise, germplasm originating from high precipitation areas may be utilized as donors of resistance genes to various grain diseases The third section investigates the potential of genomic selection (GS) in germplasm improvement. The study utilized grain-related and phenological data from Ethiopian sorghum core collection. Low to moderate prediction and validation accuracies were observed for the traits and increasing training size increased prediction accuracy. The focused identification of germplasm sampling (FIGS) approach, which had been proved successful in increasing the success rate in identifying rare alleles from large germplasm collections, was also evaluated for its complementarity with GS. Grain weight was utilized as a proxy for assessing the approach. Sampling using the FIGS-based approach changed population parameters relative to the base population. Genomic prediction on a reference population sampled using FIGS based approach had smaller validation accuracy and selection differential than randomly reconstituted reference populations. Modifying the FIGS sampling strategy by incorporating a few individuals from the opposite end of the FIGS predicted environment improved the overall performance of the system. The last chapter investigated the importance of pre-processing method to improve protein digestibility, a critical constraint in sorghum. This was conducted using four preprocessing methods on four selected varieties of sorghum varying in grain quality attributes. The result showed significant pre-processing and variety interaction effects in protein digestibility of fermented and cooked sorghum food samples, implying that varietal selection should target a specific pre-processing method. Sprouting, one of the pre-treatment methods studied, improved overall grain protein digestibility. Genotypes with inherently improved protein content and in-vitro protein digestibility when subjected to appropriate milling and pre-processing treatment can significantly enhance protein availability from fermented sorghum foods. In conclusion, understanding the adaptation history and the target end-user application is crucial for improving sorghum grain quality and nutritional traits. The information generated on the grain attributes and the genomic selection pipeline for the FIGS approach has promising potential to accelerate the development of nutritionally improved and locally adapted varieties.

Description

Keywords

sorghum, germplasm improvement, genome environment association, genome wide association study, genomic selection

Graduation Month

May

Degree

Doctor of Philosophy

Department

Department of Agronomy

Major Professor

Tesfaye Tesso

Date

2023

Type

Dissertation

Citation