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.

Isolation of a Novel Lodging Resistance QTL Gene Involved in Strigolactone Signaling and Its Pyramiding with a QTL Gene Involved in Another Mechanism

Lodging has been a major roadblock to attaining increased crop productivity. In an attempt to understand the mechanism for culm strength in rice, we isolated an effective quantitative trait locus （QTL）, STRONG CULM3 （SCM3）, the causal gene of which is identical to rice TEOSINTE BRANCHED1 （OsTB1）, a gene previously reported to positively control strigolactone （SL） signaling. A near-isogenic line （NIL） carrying SCM3 showed enhanced culm strength and increased spikelet number despite the expected decrease in tiller number, indicating that SL also has a positive role in enhancing culm strength and spikelet number. We produced a pyramiding line carrying SCM3 and SCM2, another QTL encoding AP01 involved in panicle development. The NIL-SCM2＋SCM3 showed a much stronger culm than NIL-SCM2 and NIL-SCM3 and an increased spikelet number caused by the additive effect of these QTLs. We discuss the importance of utilizing suitable alleles of these STRONG CULM QTLs without inducing detrimental traits for breeding.

OsIDD2, a zinc finger and INDETERMINATE DOMAIN protein, regulates secondary cell wall formation

Previously, we found 123 transcription factors（TFs） as candidate regulators of secondary cell wall（SCW）formation in rice by using phylogenetic and co-expression network analyses. Among them, we examined in this work the role of OsIDD_2, a zinc finger and indeterminate domain（IDD） family TF. Its overexpressors showed dwarfism, fragile leaves, and decreased lignin content, which are typical phenotypes of plants defective in SCW formation, whereas its knockout plants showed slightly increased lignin content.The RNA-seq and quantitative reverse transcription polymerase chain reaction analyses confirmed that some lignin biosynthetic genes were downregulated in the OsIDD_2-overexpressing plants, and revealed the same case for other genes involved in cellulose synthesis and sucrose metabolism. The transient expression assay using rice protoplasts revealed that OsIDD_2 negatively regulates the transcription of genes involved in lignin biosynthesis, cinnamyl alcohol dehydrogenase 2 and 3（CAD_2 and 3）, and sucrose metabolism, sucrose synthase 5（SUS_5）, whereas an Alpha Screen assay, which can detect the interaction between TFs and their target DNA sequences, directly confirmed the interaction between OsIDD_2 and the target sequences located in the promoter regions of CAD_2 and CAD_3. Based on these observations, we conclude that OsIDD_2 is negatively involved in SCW formation and other biological events by downregulating its target genes.

Is one-line hybrid rice coming?

Asian cultivated rice is one of the most important cereal crops and feeds half of the world’s population,especially in eastern and southeastern Asian countries(Virmani 2012).It is estimated that about 20%or more increase in rice production would be likely needed in the next 20 years due to the growing population and environmental changes(Virmani 2012).

Future Strategy of Breeding:Learn by Two Important Genes of Miracle Rice

In the"Analects of Confucius",there is a classic sentence that"too much is as bad as too little".The work by Wang et al.(2020)published in this issue reminds us that crop breeders should bear this sentence in mind when breed new varieties by molecular-based techniques.