Genetic dissection of grain traits and their corresponding heterosis in an elite hybrid

Sundus Zafar; Hui You; Fan Zhang; Shuang Bin Zhu; Kai Chen; Congcong Shen; Hezhou Wu; Fangjin Zhu; Conghe Zhang; Jianlong Xu

doi:10.3389/fpls.2022.977349

Genetic dissection of grain traits and their corresponding heterosis in an elite hybrid

Front Plant Sci. 2022 Oct 5:13:977349. doi: 10.3389/fpls.2022.977349. eCollection 2022.

Authors

Sundus Zafar¹, Hui You², Fan Zhang², Shuang Bin Zhu¹, Kai Chen¹, Congcong Shen¹, Hezhou Wu³, Fangjin Zhu³, Conghe Zhang⁴, Jianlong Xu^{1

2

5}

Affiliations

¹ Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
² The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
³ Hunan Tao-Hua-Yuan Agricultural Technologies Co., LTD., Hunan, China.
⁴ Win-All Hi-Tech Seed Co., Ltd., Hefei, China.
⁵ Hainan Yazhou Bay Seed Lab/National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China.

Abstract

Rice productivity has considerably improved due to the effective employment of heterosis, but the genetic basis of heterosis for grain shape and weight remains uncertain. For studying the genetic dissection of heterosis for grain shape/weight and their relationship with grain yield in rice, quantitative trait locus (QTL) mapping was performed on 1,061 recombinant inbred lines (RILs), which was developed by crossing xian/indica rice Quan9311B (Q9311B) and Wu-shan-si-miao (WSSM). Whereas, BC₁F₁ (a backcross F₁) was developed by crossing RILs with Quan9311A (Q9311A) combined with phenotyping in Hefei (HF) and Nanning (NN) environments. Overall, 114 (main-effect, mQTL) and 359 (epistatic QTL, eQTL) were identified in all populations (RIL, BC₁F₁, and mid-parent heterosis, H_MPs) for 1000-grain weight (TGW), grain yield per plant (GYP) and grain shape traits including grain length (GL), grain width (GW), and grain length to width ratio (GLWR). Differential QTL detection revealed that all additive loci in RILs population do not show heterotic effects, and few of them affect the performance of BC₁F₁. However, 25 mQTL not only contributed to BC₁F₁'s performance but also contributed to heterosis. A total of seven QTL regions was identified, which simultaneously affected multiple grain traits (grain yield, weight, shape) in the same environment, including five regions with opposite directions and two regions with same directions of favorable allele effects, indicating that partial genetic overlaps are existed between different grain traits. This study suggested different approaches for obtaining good grain quality with high yield by pyramiding or introgressing favorable alleles (FA) with the same direction of gene effect at the QTL regions affecting grain shape/weight and grain yield distributing on different chromosomes, or introgressing or pyramiding FA in the parents instead of fixing additive effects in hybrid as well as pyramiding the polymorphic overdominant/dominant loci between the parents and eliminating underdominant loci from the parents. These outcomes offer valuable information and strategy to develop hybrid rice with suitable grain type and weight.

Keywords: grain shape; grain weight; grain yield; heterosis; pyramiding breeding; quantitative trait locus/loci (QTL).