High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations

Cassava (Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America, and its starchy roots provide nourishment for 800 million people worldwide. Although native to South America, cassava was brought to Africa 400–500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for pathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map for M. esculenta Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype. We used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selectionenhanced breeding of this important crop.Bill and Melinda Gates Foundation (BMGF) Grant OPPGD1493. University of Arizona. CGIAR Research Program on Roots, Tubers, and Bananas. Next Generation Cassava Breeding grant OPP1048542 from BMGF and the United Kingdom Department for International Development. BMGF grant OPPGD1016 to IITA. National Institutes of Health S10 Instrumentation Grants S10RR029668 and S10RR027303.http://www.g3journal.orghb201

QTL mapping for pest and disease host plant resistance in cassava cultivars Kiroba and AR37-80 and coincidence of QTL with introgression regions from Manihot glaziovii

Cassava (Manihot esulenta Crantz.) is a staple food crop for more than 800 million people worldwide. It is drought tolerant and offers a flexible harvesting regime since the roots can remain in the soil and be harvested when needed. It is a food security crop when cereal crops fail. Biotic and abiotic stresses including pest and diseases negate this potential. Its heterozygous nature, long growing cycle and low seed yield per pollination poses challenges in breeding. In addition, it is highly outcrossing making it difficult to develop an adequately sized F2 population hence limiting genetic studies to F1 progenies. Cassava brown streak disease (CBSD) has emerged to be the great threat to cassava production reducing useable roots or leading to total crop loss, and if not checked it can impact more than 200 million people in Africa who depend on the crop for their food and income generation. The plausible approach to combat CBSD is to combine breeding for host plant resistance with sanitation measures and the planting of virus-free stakes. The breeding for host plant resistance should be performed as quickly and efficiently as possible, taking advantage of genomic, transformation and molecular marker technology. Conventional breeding, which does not use data generated from molecular tools, takes up to 10 years to deliver a new cultivar since the plants have to be grown for 12 months before selection can be made. If molecular markers were found to be associated with field resistance, then F1 progeny generated in a breeding program could be screened and selected at the seedling stage, thereby drastically reducing the breeding cycle and providing an accurate way of efficiently pyramiding resistance from different sources. In this project, quantitative trait loci (QTL) mapping for resistance to CBSD, cassava Mosaic disease (CMD), and cassava green mites (CGM) was performed using an F1 mapping population developed between CBSD resistant Tanzanian landrace, Kiroba, and a susceptible breeding clone, AR37-80. This aimed to construct a SNP based linkage map using the segregating population and provide a tool to identify QTL. The study investigated the presence of genomic regions in Kiroba derived from M. glaziovii and their contribution to the field resistance observed in Kiroba. The introgression regions in Kiroba were compared to those from Namikonga, the well-known CBSD resistant cultivar and other genotypes of African origin to understand the source of their resistance. The results show that only two QTL are linked to CBSD root necrosis and are located on chromosomes V and XII, while seven are associated with CBSD foliar symptoms only and are located on chromosomes IV, VI, XVII, and XVIII. The QTL on chromosomes XI and XV are linked with both CBSD foliar and root necrosis symptoms. Two QTL found on chromosome XII and XIV are linked to CMD, while two QTL located on chromosomes V and X are linked to CGM resistance. The analysis of introgression regions in Kiroba revealed the existence of large Manihot glaziovii like regions on chromosome I, XVII, and XVIII. The introgression segments on chromosomes XVII and XVIII overlap with QTL associated with CBSD foliar symptoms. These regions contain domains associated with host plant disease resistance. The introgression region on chromosome I in Kiroba is of a different haplotype to the characteristic “Amani haplotype” found in the landrace Namikonga and other genotypes analyzed in this study. Kiroba also does not have a large introgression block on chromosome IV found in other genotypes. Kiroba is closely related to a sampled Tanzanian “tree cassava.” This supports the observation that some of the QTL associated with CBSD resistance in Kiroba are different to those observed in Namikonga. This study provides an understanding of the genetic basis of the field resistance observed in the local cassava landraces, the genomic regions contributing to the resistance and the source of the resistance. This information is valuable in pyramiding QTL for host plant disease resistance.Thesis (PhD)--University of Pretoria, 2019.GeneticsPhDUnrestricte

QTL mapping for pest and disease resistance in cassava and coincidence with some introgression regions derived from M. glaziovii

Open Access Journal; Published online: 21 July 2017Genetic mapping of quantitative trait loci (QTL) for resistance to cassava brown streak disease (CBSD), cassava mosaic disease (CMD), and cassava green mite (CGM) was performed using an F1 cross developed between the Tanzanian landrace, Kiroba, and a breeding line, AR37-80. The population was evaluated for two consecutive years in two sites in Tanzania. A genetic linkage map was derived from 106 F1 progeny and 1,974 SNP markers and spanned 18 chromosomes covering a distance of 1,698 cM. Fifteen significant QTL were identified; two are associated with CBSD root necrosis only, and were detected on chromosomes V and XII, while seven were associated with CBSD foliar symptoms only and were detected on chromosomes IV, VI, XVII, and XVIII. QTL on chromosomes 11 and 15 were associated with both CBSD foliar and root necrosis symptoms. Two QTL were found to be associated with CMD and were detected on chromosomes XII and XIV, while two were associated with CGM and were identified on chromosomes V and X. There are large Manihot glaziovii introgression regions in Kiroba on chromosomes I, XVII, and XVIII. The introgression segments on chromosomes XVII and XVIII overlap with QTL associated with CBSD foliar symptoms. The introgression region on chromosome I is of a different haplotype to the characteristic “Amani haplotype” found in the landrace Namikonga and others, and unlike some other genotypes, Kiroba does not have a large introgression block on chromosome IV. Kiroba is closely related to a sampled Tanzanian “tree cassava.” This supports the observation that some of the QTL associated with CBSD resistance in Kiroba are different to those observed in another variety, Namikonga