@article{Faruquee2021, 
author = {Muhiuddin Faruquee and Qiang Zhang and Lubiao Zhang and Linyun Xu and Wensheng Wang and Jiansan Chen and Jianlong Xu and Zhikang Li and Binying Fu and Tianqing Zheng},
title = {Dominant early heading without yield drag in a sister-line BC breeding progeny DEH_229 is controlled by multiple genetic factors with main-effect loci},
year = {2021},
journal = {The Crop Journal},
volume = {9},
number = {2},
pages = {400-411},
keywords = {Dominant early heading, Yield drag, Sister-line BC breeding, Multiple genetic factors, Cryptic genetic variation (CGV), Rice (Oryza sativa L.)},
url = {https://www.sciopen.com/article/10.1016/j.cj.2020.06.014},
doi = {10.1016/j.cj.2020.06.014},
abstract = {Dominant early heading (DEH) in rice (Oryza sativa L.) is of interest in both breeding and genetics. The genetic mechanisms underlying DEH have remained largely unclear. We have developed a near-isogenic DEH line without yield drag named DEH_229 by sister-line backcross (BC) breeding with MH63, a restorer, as the genetic background. We conducted a pilot genetic investigation under both short-day (SD) and long-day (LD) conditions. The DEH line harbored only 1.06% variation in the genome sequence relative to MH63. The variants were distributed throughout the genome. Using QTL mapping by sequencing (QTL-seq) on an F2 population derived from a cross of MH63 × DEH_229, 57 loci were detected under the SD condition. Joint mapping employing a genome-wide association study with accessions from the 3000 rice genome sequencing project (3K-RG), reduced the number of QTL by 43.9%. Using Rice Functional Genomics & Breeding (RFGB) database, the number of SNP cluster regions within the QTL regions reduced by 27.3%. Further comparison of the genome variation between DEH_229 and MH63 in addition to gene annotation information revealed a new DEH allele of DTH3 with multiple variable sites as a possible major factor underlying the early-heading phenotype of DEH_229. An InDel marker, ZMEH_1, was designed based on the variation between DEH_229 and MH63 within this region. It accounted for 86.0% of heading date variation under both SD and LD conditions in 109 randomly chosen progeny derived from extreme lines of the MH63 × DEH_229 population. This study reveals the genetic complexity of DEH in the near-isogenic line and may provide useful material and marker information for plant molecular breeding.}
}