Rapid identification of a candidate nicosulfuron sensitivity gene ( Nss ) in maize ( Zea mays L.) via combining bulked segregant analysis and RNA-seq

Key message A candidate nicosulfuron sensitivity gene Nss was identified by combining bulked segregant analysis and RNA-seq. Multiple mutations of this gene were discovered in nicosulfuron-sensitive maize compared with the tolerant. Abstract It has been demonstrated that variabilities exist in maize response to nicosulfuron. Two nicosulfuron-sensitive inbred lines (HB39, HB41) and two tolerant inbred lines (HB05, HB09) were identified via greenhouse and field trials. Genetic analysis indicated that the sensitivity to nicosulfuron in maize was controlled by a single, recessive gene. To precisely and rapidly map the nicosulfuron sensitivity gene ( Nss ), two independent F 2 segregating populations, Population A (HB41 × HB09) and Population B (HB39 × HB05), were constructed. By applying bulked segregant RNA-Seq (BSR-Seq), the Nss gene was, respectively, mapped on the short arm of chromosome 5 (chr5: 1.1–15.3 Mb) and (chr5: 0.5–18.2 Mb) using two populations, with 14.2 Mb region in common. Further analysis revealed that there were 43 and 119 differentially expressed genes in the mapping intervals, with 18 genes in common. Gene annotation results showed that a cytochrome P450 gene ( CYP81A9 ) appeared to be the candidate gene of Nss associated with nicosulfuron sensitivity in maize. Sequence analysis demonstrated that two common deletion mutations existed in the sensitive maize, which might lead to the nicosulfuron sensitivity in maize. The results will make valuable contributions to the understanding of molecular mechanism of herbicide sensitivity in maize.