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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #333324

Research Project: Development and Application of Genetic, Genomic, and Bioinformatic Resources in Maize

Location: Plant, Soil and Nutrition Research

Title: Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

Author
item RAMU, PUNNA - CORNELL UNIVERSITY - NEW YORK
item ESUMA, WILLIAMS - INTERNATIONAL CROPS RESEARCH INSTITUTE FOR SEMI-ARID TROPICS (ICRISAT) - NIGERIA
item KAWUKI, ROBERT - INTERNATIONAL CROPS RESEARCH INSTITUTE FOR SEMI-ARID TROPICS (ICRISAT) - NIGERIA
item RABBI, ISMAIL - INTERNATIONAL INSTITUTE OF TROPICAL AGRICULTURE (IITA)
item EGESI, CHIEDOZIE - NATIONAL ROOT CROPS RESEARCH INSTITUTE (NRCRI)
item BREDESON, JESSEN - UNIVERSITY OF CALIFORNIA
item BART, REBECCA - DANFORTH PLANT SCIENCE CENTER
item VERMA, JANU - CORNELL UNIVERSITY - NEW YORK
item Buckler, Edward - Ed
item LU, FEI - CORNELL UNIVERSITY - NEW YORK

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/21/2017
Publication Date: 4/17/2017
Citation: Ramu, P., Esuma, W., Kawuki, R., Rabbi, I., Egesi, C., Bredeson, J., Bart, R., Verma, J., Buckler IV, E.S., Lu, F. 2017. Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nature Genetics. 49:959-963.

Interpretive Summary: Cassava is an important staple food crop in Africa and Latin America, feeding hundreds of millions people. However, constantly emerging deleterious mutations may rapidly accumulate via clonal propagation and severely reduce its productivity. We characterized the genetic load of cassava in this study, which was the first time deleterious mutations have been evaluated in a clonally propagated species. By deep sequencing a comprehensive and representative collection of 241 cassava accessions, we developed the HapMapII, a highly valuable resource for cassava genetic studies and breeding. The molecular evidence indicates that cassava is becoming progressively sicker genetically, while breeders are working hard to make hybrid that lessen these effects. This study provides a tremendous resources for geneticists and breeders working in cassava, and recommend that new approaches for breeding cassava are needed.

Technical Abstract: Cassava (Manihot esculenta Crantz) is an important staple food crop in Africa and South America whose fitness may be severely reduced by ubiquitous deleterious variation. To evaluate these deleterious mutations in cassava genome, we constructed a cassava haplotype map by deep sequencing of 241 diverse accessions and identified over 30 million segregating variants. While domestication modified starch and ketone metabolism pathways for human consumption, the concomitant bottleneck and clonal propagation resulted in a large proportion of fixed deleterious amino acid changes, raising the number of deleterious mutations by 24%, and shifting the mutational burden towards common variants. Deleterious mutations in this clonally propagated crop are ineffectively purged due to limited recombination. Recent breeding efforts in cassava maintained the yield by masking the harmful effects of deleterious mutations through shielding the most damaging recessive mutations in heterozygous state, but failed to purge the load, which should be a key target for future cassava breeding.