Deciphering the enigmatic spikelet traits:Resolving trade-offs for enhancing rice yield

Increasing the yield is one of the most important goals of crop improvement.Since the beginning of rice cultivation thousands of years ago,many efforts have been made to increase rice yield.One of the successes in this history was the Green Revolution.This tremendous improvement in the 1960s was achieved by increasing rice and wheat production through the development and widespread adoption of semi-dwarf varieties with the extensive use of fertilizers(Hedden,2003).Dwarfism in crops lowers the center of gravity of the plant body,reducing the risk of lodging and enabling farmers to use more fertilizer to increase yields.Semi-dwarf mutations in both rice and wheat created during the Green Revolution are related to the plant growth hormone gibberellin(GA).Although other mechanisms cause dwarf mutants,only GA-related semi-dwarf mutants were selected during the Green Revolution(Wang et al.,2021).While GA-related abnormalities only make plants shorter,most cases caused by other mechanisms involve not only dwarfism but also other morphological abnormalities.

Integrated genome-wide differentiation and association analyses identify causal genes underlying breeding-selected grain quality traits in japonica rice

Improving grain quality is a primary objective in contemporary rice breeding.Japanese modern rice breeding has developed two different types of rice,eating and sake-brewing rice,with different grain characteristics,indicating the selection of variant gene alleles during the breeding process.Given the critical importance of promptly and efficiently identifying genes selected in past breeding for future molecular breeding,we conducted genome scans for divergence,genome-wide association studies,and map-based cloning.Consequently,we successfully identified two genes,OsMnS and OsWOX9D,both contributing to rice grain traits.OsMnS encodes a mannan synthase that increases the white core frequency in the endosperm,a desirable trait for sake brewing but decreases the grain appearance quality.OsWOX9D encodes a grass-specific homeobox-containing transcription factor,which enhances grain width for better sake brewing.Furthermore,haplotype analysis revealed that their defective alleles were selected in East Asia,but not Europe,during modern improvement.In addition,our analyses indicate that a reduction in grain mannan content during African rice domestication may also be caused a defective OsMnS allele due to breeding selection.This study not only reveals the delicate balance between grain appearance quality and nutrition in rice but also provides a new strategy for isolating causal genes underlying complex traits,based on the concept of“breeding-assisted genomics”in plants.