A Rare Allele of GS2 Enhances Grain Size anc Grain Yield in Rice

Grain size determines grain weight and affects grain quality. Several major quantitative trait loci （QTLs） regulating grain size have been cloned; however, our understanding of the underlying mechanism that regulates the size of rice grains remains fragmentary. Here, we report the cloning and characterization of a dominant QTL, GRAIN SIZE ON CHROMOSOME 2 （GS2）, which encodes Growth-Regulating Factor 4 （OsGRF4）, a transcriptional regulator. GS2 localizes to the nucleus and may act as a transcription activator. A rare mutation of GS2 affecting the binding site of a microRNA, OsmiR396c, causes elevated expression of GS2/OsGRF4. The increase in GS2 expression leads to larger cells and increased numbers of cells, which thus enhances grain weight and yield. The introduction of this rare allele of GS2/OsGRF4 into rice cultivars could significantly enhance grain weight and increase grain yield, with possible applications in breeding high-yield rice varieties.

A Strigolactone Biosynthesis Gene Contributed to the Green Revolution in Rice

Plant architecture is a complex agronomic trait and a major factor of crop yield,which is affected by several important hormones.Strigolactones(SLs)are identified as a new class hormoneinhibiting branching in many plant species and have been shown to be involved in various developmental processes.Genetical and chemical modulation of the SL pathway is recognized as a promising approach to modify plant architecture.However,whether and how the genes involved in the SL pathway could be utilized in breeding still remain elusive.Here,we demonstrate that a partial loss-of-function allele of the SL biosynthesis gene,HIGH TILLERING AND DWARF 1/DWARF17(HTD1/D17),which encodes CAROTENOID CLEAVAGE DIOXYGENASE 7(CCD7),increases tiller number and improves grain yield in rice.We found that the HTD1 gene had been widely utilized and co-selected with Semidwarf 1(SD1),both contributing to the improvement of plant architecture in modern rice varieties since the Green Revolution in the 1960s.Understanding how phytohormone pathway genes regulate plant architecture and how they have been utilized and selected in breeding will lay the foundation for developing the rational approaches toward improving crop yield.

High-quality genome assembly of Huazhan and Tianfeng,the parents of an elite rice hybrid Tian-you-hua-zhan

High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding.Tian-you-hua-zhan has been a leading hybrid in China over the past decade.Here,de novo genome assembly strategy optimization for the rice indica lines Huazhan(HZ)and Tianfeng(TF),including sequencing platforms,assembly pipelines and sequence depth,was carried out.The PacBio and Nanopore platforms for long-read se-quencing were utilized,with the Canu,wtdbg2,SMARTdenovo,Flye,Canu-wtdbg2,Canu-SMARTdenovo and Canu-Flye assemblers.The combination of PacBio and Canu was optimal,considering the contig N50 length,contig number,assembled genome size and polishing process.The assembled contigs were scaffolded with Hi-C data,resulting in two“golden quality”rice reference genomes,and evaluated using the scaffold N50,BUSCO,and LTR assembly index.Furthermore,42,625 and 41,815 non-transposable element genes were annotated for HZ and TF,respectively.Based on our assembly of HZ and TF,as well as Zhenshan97,Minghui63,Shuhui498 and 9311,comprehensive variations were identified using Nipponbare as a reference.The de novo assembly strategy for rice we optimized and the“golden quality”rice genomes we produced for HZ and TF will benefit rice genomics and breeding research,especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.