Yu Hang, Shahid Muhammad Qasim, Li Qihang, Li Yudi, Li Cong, Lu Zijun, Wu Jinwen, Zhang Zemin, Liu Xiangdong
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.
Rice (N Y). 2020 Jun 3;13(1):32. doi: 10.1186/s12284-020-00387-3.
Neo-tetraploid rice (NTR) is a new tetraploid rice germplasm that developed from the crossing and directional selection of different autotetraploid rice lines, which showed high fertility and promising yield potential. However, systematic yield assessment, genome composition and functional variations associated with fertility and yield remain elusive.
Two season's field trials of 15 NTRs and 27 autotetraploid rice (ATR) lines revealed that the improvement of YPP (yield per plant, 4.45 g increase) were significantly associated with the increase of SS (seed setting, 29.44% increase), and yield and seed setting of NTRs improved significantly compared to parental lines. Whole genome resequencing of 13 NTR sister lines and their parents at about 48.63 depth were conducted and genome compositions were illustrated using inherited chromosomal blocks. Interestingly, 222 non-parental genes were detected between NTRs and their low fertility parental lines, which were conserved in 13 NTRs. These genes were overlapped with yield and fertility QTLs, and RNA-Seq analysis revealed that 81 of them were enriched in reproductive tissues. CRISPR/Cas9 gene knockout was conducted for 9 non-parental genes to validate their function. Knockout mutants showed on an average 25.63% and 4.88 g decrease in SS and YPP, respectively. Notably, some mutants showed interesting phenotypes, e.g., kin7l (kinesin motor gene) and kin14m (kinesin motor gene), bzr3 (BES1/BZR1 homolog) and nrfg4 (neo-tetraploid rice fertility related gene) exhibited 44.65%, 24.30%, 24.42% and 28.33% decrease in SS and 8.81 g, 4.71 g, 5.90 g, 6.22 g reduction in YPP, respectively.
Comparative genomics provides insights into genome composition of neo-tetraploid rice and the genes associated with fertility and yield will play important role to reveal molecular mechanisms for the improvement of tetraploid rice.
新型四倍体水稻（NTR）是一种新的四倍体水稻种质，由不同的同源四倍体水稻品系杂交和定向选择培育而成，表现出高育性和良好的产量潜力。然而，与育性和产量相关的系统产量评估、基因组组成及功能变异仍不清楚。
对15个新型四倍体水稻和27个同源四倍体水稻品系进行了两季田间试验，结果表明单株产量（YPP）的提高（增加4.45克）与结实率（SS）的增加（提高29.44%）显著相关，且新型四倍体水稻的产量和结实率相比亲本有显著提高。对13个新型四倍体水稻姊妹系及其亲本进行了约48.63深度的全基因组重测序，并利用遗传染色体片段展示了基因组组成。有趣的是，在新型四倍体水稻及其低育性亲本之间检测到222个非亲本基因，这些基因在13个新型四倍体水稻中保守。这些基因与产量和育性QTL重叠，RNA测序分析表明其中81个基因在生殖组织中富集。对9个非亲本基因进行了CRISPR/Cas9基因敲除以验证其功能。敲除突变体的结实率和单株产量平均分别降低25.63%和4.88克。值得注意的是，一些突变体表现出有趣的表型，例如，kin7l（驱动蛋白基因）和kin14m（驱动蛋白基因）、bzr3（BES1/BZR1同源基因）和nrfg4（新型四倍体水稻育性相关基因）的结实率分别降低44.65%、24.30%、24.42%和28.33%，单株产量分别降低8.81克、4.71克、5.90克和6.22克。
比较基因组学为新型四倍体水稻的基因组组成提供了见解，与育性和产量相关的基因将在揭示四倍体水稻改良的分子机制中发挥重要作用。
