Identification and haplotype analysis of SiCHLI: a gene for yellow-green seedling as morphological marker to accelerate foxtail millet (Setaria italica) hybrid breeding.

ABSTRACT

KEY MESSAGE We cloned and developed functional markers for the SiCHLI gene, which is responsible for the yellow-green color of leaves in foxtail millet, a frequently used marker trait in the hybrid breeding of foxtail millet by using bulked segregant analysis sequencing and haplotype analysis on the F2 and core-collected nature populations. The color of leaves has been widely used as a marker for the hybrid breeding of foxtail millet; however, few related gene have been cloned to date. Here, we used two F2 populations generated from crosses between the highly male-sterile material 125A with yellow-green leaves, and CG58 and S410, which have green leaves, to identify the genes underlying the yellow-green color of the leaves of foxtail millet. The leaves of 125A seedlings were yellow-green, but they became green at the heading stage. The content of chlorophyll a and chlorophyll b was lower, the number of thylakoid lamellae and grana was reduced, and the chloroplasts was more rounded in 125A than in S410 at the yellow-green leaf stage; however, no differences were observed between 125A and S410 in these traits and photosynthetic at the heading stage. Bulked segregant analysis and map-based cloning revealed that the SiCHLI gene is responsible for the leaf colors of 125A. A nonsynonymous mutation (C/T) in exon 3 causes yellow-green leaves in 125A at the seedling stage. Haplotype analysis of the SiCHLI gene in 596 core collected accessions revealed a new haplotype associated with high photosynthetic metabolic potential at the heading and mature stages, which could be used to enhance sterile lines with yellow-green leaves. We developed a functional marker that will facilitate the identification of foxtail millet accessions with the different types of yellow-green leaves. Generally, our study provides new genetic resources to guide the future marker-assisted or target-base editing in foxtail millet hybrid breeding.