Enhanced Expression of QTL qLL9/DEP1 Facilitates the Improvement of Leaf Morphology and Grain Yield in Rice
Xue Fu ?, Jing Xu ?, Mengyu Zhou, Minmin Chen, Lan Shen, Ting Li, Yuchen Zhu, JiajiaWang,Jiang Hu, Li Zhu, Zhenyu Gao, Guojun Dong, Longbiao Guo, Deyong Ren, Guang Chen ,Jianrong Lin, Qian Qian * and Guangheng Zhang *
International Journal of Molecular Sciences
10.3390/ijms20040866
Abstract
In molecular breeding of super rice, it is essential to isolate the best quantitative trait loci
(QTLs) and genes of leaf shape and explore yield potential using large germplasm collections and
genetic populations. In this study, a recombinant inbred line (RIL) population was used, which was
derived from a cross between the following parental lines: hybrid rice Chunyou84, that is, japonica
maintainer line Chunjiang16B (CJ16); and indica restorer line Chunhui 84 (C84) with remarkable
leaf morphological differences. QTLs mapping of leaf shape traits was analyzed at the heading
stage under different environmental conditions in Hainan (HN) and Hangzhou (HZ). A major QTL
qLL9 for leaf length was detected and its function was studied using a population derived from
a single residual heterozygote (RH), which was identified in the original population. qLL9 was
delimitated to a 16.17 kb region flanked by molecular markers C-1640 and C-1642, which contained
three open reading frames (ORFs). We found that the candidate gene for qLL9 is allelic to DEP1
using quantitative real-time polymerase chain reaction (qRT-PCR), sequence comparison, and the
clustered regularly interspaced short palindromic repeat-associated Cas9 nuclease (CRISPR/Cas9)
genome editing techniques. To identify the effect of qLL9 on yield, leaf shape and grain traits were
measured in near isogenic lines (NILs) NIL-qLL9CJ16 and NIL-qLL9C84, as well as a chromosome
segment substitution line (CSSL) CSSL-qLL9KASA with a Kasalath introgressed segment covering
qLL9 in the Wuyunjing (WYJ) 7 backgrounds. Our results showed that the flag leaf lengths of
NIL-qLL9C84 and CSSL-qLL9KASA were significantly different from those of NIL-qLL9CJ16 and WYJ
7, respectively. Compared with NIL-qLL9CJ16, the spike length, grain size, and thousand-grain
weight of NIL-qLL9C84 were significantly higher, resulting in a significant increase in yield of 15.08%.
Exploring and pyramiding beneficial genes resembling qLL9C84 for super rice breeding could increase
both the source (e.g., leaf length and leaf area) and the sink (e.g., yield traits). This study provides
a foundation for future investigation of the molecular mechanisms underlying the source–sink
balance and high-yield potential of rice, benefiting high-yield molecular design breeding for global
food security.