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DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom
Author(s) -
Demirci Sevgin,
Peters Sander A.,
Ridder Dick,
Dijk Aalt D.J.
Publication year - 2018
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13979
Subject(s) - biology , oryza sativa , arabidopsis , arabidopsis thaliana , solanum , genome , genetics , meiosis , dna sequencing , dna , genomic dna , computational biology , gene , botany , mutant
Summary A better understanding of genomic features influencing the location of meiotic crossovers ( CO s) in plant species is both of fundamental importance and of practical relevance for plant breeding. Using CO positions with sufficiently high resolution from four plant species [ Arabidopsis thaliana , Solanum lycopersicum (tomato), Zea mays (maize) and Oryza sativa (rice)] we have trained machine‐learning models to predict the susceptibility to CO formation. Our results show that CO occurrence within various plant genomes can be predicted by DNA sequence and shape features. Several features related to genome content and to genomic accessibility were consistently either positively or negatively related to CO s in all four species. Other features were found as predictive only in specific species. Gene annotation‐related features were especially predictive for maize, whereas in tomato and Arabidopsis propeller twist and helical twist ( DNA shape features) and AT / TA dinucleotides were found to be the most important. In rice, high roll (another DNA shape feature) and low CA dinucleotide frequency in particular were found to be associated with CO occurrence. The accuracy of our models was sufficient for Arabidopsis and rice (area under receiver operating characteristic curve, AUROC > 0.5), and was high for tomato and maize ( AUROC ≫ 0.5), demonstrating that DNA sequence and shape are predictive for meiotic CO s throughout the plant kingdom.