Current status and impending progress for cassava structural genomics

Lyons, Jessica B.; Bredeson, Jessen V.; Mansfeld, Ben N.; Bauchet, Guillaume; Berry, Jeffrey C.; Boyher, Adam; Mueller, Lukas A.; Rokhsar, Daniel S.; Bart, Rebecca

doi:10.1007/s11103-020-01104-w

Cited by 12 publications

(6 citation statements)

References 89 publications

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“…Recent attempts at assembling heterozygous farmer‐preferred cassava lines have produced contiguous large assemblies (Kuon et al., 2019 ). These assemblies, however, are limited due to the lack of haplotypic separation; the primary assemblies include both haplotypes and thus contain many duplicated sequences (Kuon et al., 2019 ; Lyons et al., 2021 ). This has implications on the assembly size and scaffolding, which can be severely impacted by these duplications (Guan et al., 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Large structural variations in the haplotype‐resolved African cassava genome

et al. 2021

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Summary Cassava (Manihot esculenta Crantz, 2n = 36) is a global food security crop. It has a highly heterozygous genome, high genetic load, and genotype‐dependent asynchronous flowering. It is typically propagated by stem cuttings and any genetic variation between haplotypes, including large structural variations, is preserved by such clonal propagation. Traditional genome assembly approaches generate a collapsed haplotype representation of the genome. In highly heterozygous plants, this results in artifacts and an oversimplification of heterozygous regions. We used a combination of Pacific Biosciences (PacBio), Illumina, and Hi‐C to resolve each haplotype of the genome of a farmer‐preferred cassava line, TME7 (Oko‐iyawo). PacBio reads were assembled using the FALCON suite. Phase switch errors were corrected using FALCON‐Phase and Hi‐C read data. The ultralong‐range information from Hi‐C sequencing was also used for scaffolding. Comparison of the two phases revealed >5000 large haplotype‐specific structural variants affecting over 8 Mb, including insertions and deletions spanning thousands of base pairs. The potential of these variants to affect allele‐specific expression was further explored. RNA‐sequencing data from 11 different tissue types were mapped against the scaffolded haploid assembly and gene expression data are incorporated into our existing easy‐to‐use web‐based interface to facilitate use by the broader plant science community. These two assemblies provide an excellent means to study the effects of heterozygosity, haplotype‐specific structural variation, gene hemizygosity, and allele‐specific gene expression contributing to important agricultural traits and further our understanding of the genetics and domestication of cassava.

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Section: Introductionmentioning

confidence: 99%

Large structural variations in the haplotype‐resolved African cassava genome

et al. 2021

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“…The cassava expression atlas was implemented on cassavabase ( https://cassavabase.org ), an open-source digital ecosystem dedicated to the cassava research community 21 , 22 . Cassavabase provides a tool suite to assist breeders and breeding programs in automating their routine breeding and pre-breeding activities.…”

Section: Resultsmentioning

confidence: 99%

A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz)

Ogbonna

Ramu

Esuma

et al. 2021

Sci Rep

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Cassava, a food security crop in Africa, is grown throughout the tropics and subtropics. Although cassava can provide high productivity in suboptimal conditions, the yield in Africa is substantially lower than in other geographies. The yield gap is attributable to many challenges faced by cassava in Africa, including susceptibility to diseases and poor soil conditions. In this study, we carried out 3’RNA sequencing on 150 accessions from the National Crops Resources Research Institute, Uganda for 5 tissue types, providing population-based transcriptomics resources to the research community in a web-based queryable cassava expression atlas. Differential expression and weighted gene co-expression network analysis were performed to detect 8820 significantly differentially expressed genes (DEGs), revealing similarity in expression patterns between tissue types and the clustering of detected DEGs into 18 gene modules. As a confirmation of data quality, differential expression and pathway analysis targeting cassava mosaic disease (CMD) identified 27 genes observed in the plant–pathogen interaction pathway, several previously identified CMD resistance genes, and two peroxidase family proteins different from the CMD2 gene. Present research work represents a novel resource towards understanding complex traits at expression and molecular levels for the development of resistant and high-yielding cassava varieties, as exemplified with CMD.

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“…However, loss of genetic diversity, deleterious mutation, and pathogen accumulation are the major pitfalls of these clonal propagation methods [ 67 ]. Furthermore, the relatively long growth period of tubers and tuberous crops is a major obstacle in the breeding process of these plants [ 68 , 69 , 70 ]. Therefore, the complete understanding of molecular mechanism that control floral formation in tubers and tuberous root crops could aid in the breeding process of these crops.…”

Section: Pebp Signaling Network In Flowering Time Regulationmentioning

confidence: 99%

PEBP Signaling Network in Tubers and Tuberous Root Crops

Susila

Purwestri²

2023

Plants

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Tubers and tuberous root crops are essential carbohydrate sources and staple foods for humans, second only to cereals. The developmental phase transition, including floral initiation and underground storage organ formation, is controlled by complex signaling processes involving the integration of environmental and endogenous cues. FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1/CENTRORADIALIS (TFL1/CEN), members of the phosphatidylethanolamine-binding protein (PEBP) gene family, play a central role in this developmental phase transition process. FT and FT-like proteins have a function to promote developmental phase transition, while TFL1/CEN act oppositely. The balance between FT and TFL1/CEN is critical to ensure a successful plant life cycle. Here, we present a summarized review of the role and signaling network of PEBP in floral initiation and underground storage organ formation, specifically in tubers and tuberous root crops. Lastly, we point out several questions that need to be answered in order to have a more complete understanding of the PEBP signaling network, which is crucial for the agronomical improvement of tubers and tuberous crops.

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Current status and impending progress for cassava structural genomics

Cited by 12 publications

References 89 publications

Large structural variations in the haplotype‐resolved African cassava genome

Large structural variations in the haplotype‐resolved African cassava genome

A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz)

PEBP Signaling Network in Tubers and Tuberous Root Crops

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