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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 #417826
Research Project: Enabling Mechanistic Allele Mining to Accelerate Genomic Selection for New Agro-Ecosystems

Location: Plant, Soil and Nutrition Research

Title: Muller’s Ratchet in Action: The Erosion of Sexual Reproduction Genes in Domesticated Cassava (Manihot esculenta)

Author
item LONG, EVAN - University Of California, Davis
item STITZER, MICHELLE - Cornell University
item SCHULZ, AIMEE - Cornell University
item ROMAY, M CINTA - Cornell University
item ROBBINS, KELLY - Cornell University
item Buckler, Edward - Ed

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 2/15/2024
Publication Date: 2/15/2024
Citation: Long, E.M., Stitzer, M., Schulz, A.J., Romay, M., Robbins, K.R., Buckler Iv, E.S. 2024. Muller’s Ratchet in Action: The Erosion of Sexual Reproduction Genes in Domesticated Cassava (Manihot esculenta). bioRxiv. https://doi.org/10.1101/2024.02.14.580345.
DOI: https://doi.org/10.1101/2024.02.14.580345

Interpretive Summary: This research explores how centuries of clonal propagation in cassava, a vital food crop, have led to the accumulation of harmful genetic mutations due to the lack of sexual reproduction. This process, known as Muller's Ratchet, has caused a significant decline in cassava's reproductive performance and overall yield, posing challenges for modern breeding programs. The study utilized advanced genomic techniques to analyze 52 cassava genomes and identify 48 genes that have become less subject to natural selection. Many of these genes are related to flower and pollen development, highlighting how domestication has reduced the evolutionary pressures on these reproductive functions. These findings suggest that targeting these genetic issues could improve cassava breeding efforts, essential for developing new varieties that can meet growing global demands

Technical Abstract: Centuries of clonal propagation in cassava (Manihot esculenta) have engaged Muller’s Ratchet, leading to the accumulation of deleterious mutations due to the absence of sexual recombination. This has resulted in both inbreeding depression affecting yield and a significant decrease in reproductive performance, creating hurdles for contemporary breeding programs. Cassava is a member of the Euphorbiaceae family, including notable species such as rubber tree (Hevea brasiliensis) and poinsettia (Euphorbia pulcherrima). Expanding upon preliminary draft genomes, we annotated 7 long-read genome assemblies and aligned a total of 52 genomes, to analyze selection across the genome and the phylogeny. Through this comparative genomic approach, we identified 48 genes under relaxed selection in cassava. Notably, we discovered an overrepresentation of floral expressed genes, especially focused at six pollen-related genes. Our results indicate that domestication and a transition to clonal propagation has reduced selection pressures on sexually reproductive functions in cassava leading to an accumulation of mutations in pollen-related genes. This relaxed selection and the genome-wide deleterious mutations responsible for inbreeding depression are potential targets for improving cassava breeding, where the generation of new varieties relies on recombining favorable alleles through sexual reproduction.