Tracking crop varieties using genotyping-by-sequencing markers: a case study using cassava (Manihot esculenta Crantz)

Abstract Recombination has essential functions in meiosis, evolution, and breeding. The frequency and distribution of crossovers dictate the generation of new allele combinations and can vary across species and between sexes. Here, we examine recombination landscapes across the 18 chromosomes of cassava (Manihot esculenta Crantz) with respect to male and female meioses and known introgressions from the wild relative Manihot glaziovii. We used SHAPEIT2 and duoHMM to infer crossovers from genotyping-by-sequencing (GBS) data and a validated multi-generational pedigree from the International Institute of Tropical Agriculture (IITA) cassava breeding germplasm consisting of 7,020 informative meioses. We then constructed new genetic maps and compared them to an existing map previously constructed by the International Cassava Genetic Map Consortium (ICGMC). We observed higher recombination rates in females compared to males, and lower recombination rates in M. glaziovii introgression segments on chromosomes 1 and 4, with suppressed recombination along the entire length of the chromosome in the case of the chromosome 4 introgression. Finally, we discuss hypothesized mechanisms underlying our observations of heterochiasmy and crossover suppression and discuss the broader implications for plant breeding.

Download Full-text

Sexual dimorphism and the effect of wild introgressions on recombination in cassava (Manihot esculenta Crantz) breeding germplasm

10.1101/2021.09.22.461431 ◽

2021 ◽

Author(s):

Jean-Luc Jannink ◽

Ariel W. Chan ◽

Seren St. Clair Villwock ◽

Amy L Williams

Keyword(s):

Manihot Esculenta ◽

Genotyping By Sequencing ◽

Genetic Maps ◽

International Institute ◽

Tropical Agriculture ◽

Recombination Rates ◽

Manihot Esculenta Crantz ◽

Suppressed Recombination ◽

Manihot Glaziovii ◽

Breeding Germplasm

Recombination has essential functions in meiosis, evolution, and breeding. The frequency and distribution of crossovers dictate the generation of new allele combinations and can vary across species and between sexes. Here, we examine recombination landscapes across the 18 chromosomes of cassava (Manihot esculenta Crantz) with respect to male and female meioses and known introgressions from the wild relative Manihot glaziovii. We used SHAPEIT2 and duoHMM to infer crossovers from genotyping-by-sequencing (GBS) data and a validated multi-generational pedigree from the International Institute of Tropical Agriculture (IITA) cassava breeding germplasm consisting of 7,020 informative meioses. We then constructed new genetic maps and compared them to an existing map previously constructed by the International Cassava Genetic Map Consortium (ICGMC). We observed higher recombination rates in females compared to males, and lower recombination rates in M. glaziovii introgression segments on chromosomes 1 and 4, with suppressed recombination along the entire length of the chromosome in the case of the chromosome 4 introgression. Finally, we discuss hypothesized mechanisms underlying our observations of heterochiasmy and crossover suppression and discuss the broader implications for plant breeding.

Download Full-text

Genetic architecture and gene mapping of cyanide in cassava (Manihot esculenta Crantz.)

10.1101/2020.06.19.159160 ◽

2020 ◽

Cited By ~ 1

Author(s):

Alex C Ogbonna ◽

Luciano Rogerio Braatz de Andrade ◽

Ismail Y. Rabbi ◽

Lukas A. Mueller ◽

Eder Jorge de Oliveira ◽

...

Keyword(s):

Gene Mapping ◽

Manihot Esculenta ◽

Genetic Architecture ◽

Allelic Variation ◽

Genotyping By Sequencing ◽

Tuber Quality ◽

Human Consumption ◽

Manihot Esculenta Crantz ◽

Breeding Lines ◽

Bitter Cassava

AbstractCassava is a root crop originating from South America and a major staple crop in the Tropics, including marginal environments. In this study, we focused on South American and African cassava germplasm and investigated the genetic architecture of Hydrogen Cyanide (HCN), a major component of tuber quality. HCN is a plant defense component against herbivory but also toxic for human consumption. We genotyped 3,354 landraces and modern breeding lines originating from 26 Brazilian states and 1,389 individuals were phenotypically characterized across multi-year trials for HCN. All plant material was subjected to high density genotyping using Genotyping-by-sequencing (GBS). We performed genome wide association mapping (GWAS) to characterize the genetic architecture and gene mapping of HCN. Field experiment revealed strong broad and narrow-sense trait heritability (0.82 and 0.41 respectively). Two major loci were identified, encoding for an ATPase and a MATE protein and contributing up to 7% and 30% of the cyanide concentration in roots, respectively. We developed diagnostic markers for breeding applications, validated trait architecture consistency in African germplasm and investigated further evidence for domestication of sweet and bitter cassava. Fine genomic loci characterization indicate; (i) a major role played by vacuolar transporter in regulating HCN content, (ii) co-domestication of sweet and bitter cassava major alleles to be geographical zone dependant, and (ii) major loci allele for high cyanide cassava in Manihot esculenta Crantz seems to originate from its ancestor, M. esculenta ssp. flabellifolia. Taken together these findings expand insights on cyanide in cassava and its glycosylated derivatives in plants.One-sentence summaryIdentification of an intracellular transporter gene and its allelic variation allow to point out cultivars with up to 30 percent decrease in cassava root cyanide content, toxic for human consumption.

Download Full-text