Identification of grain shape determining genes can facilitate breeding of rice cultivars with optimal grain shape and appearance quality. Here, we identify GS9 (Grain Shape Gene on Chromosome 9) gene by map-based cloning. The gs9 null mutant has slender grains, while overexpression GS9 results in round grains. GS9 encodes a protein without known conserved functional domain. It regulates grain shape by altering cell division. The interaction of GS9 and ovate family proteins OsOFP14 and OsOFP8 is modulated by OsGSK2 kinase, a key regulator of the brassinosteroids signaling pathway. Genetic interaction analysis reveals that GS9 functions independently from other previously identified grain size genes. Introducing the gs9 allele into elite rice cultivars significantly improves grain shape and appearance quality. It suggests potential application of gs9, alone or in combination with other grain size determining genes, in breeding of rice varieties with optimized grain shape.

The gelatinization temperature (GT) of endosperm starch influences rice eating and the cooking quality (ECQ). ALK encoding soluble starch synthase IIa (SSIIa) is the major gene determining grain GT in rice. Herein, we identified a spontaneous ALK mutant named ALK d , which resulted from a G/T single-nucleotide polymorphism (SNP) in exon 1 of the ALK c allele from the high-GT indica rice cultivar. Compared with grains from the ALK c near-isogenic line (NIL), NIL(ALK d ) grains exhibited a high GT (2.3 °C) and improved retrogradation properties. The NIL(ALK d ) grain starch contained an increased proportion of amylopectin intermediate chains (DP 13−24) at the expense of short chains (DP < 12), resulting in enhancements in both the crystallinity and the lamellar peak intensity compared with low-GT rice grains. Moreover, both NIL(ALK d ) and NIL(ALK c ) grains also featured a significantly lower apparent amylose content (AAC), harder gel consistency (GC), higher pasting curve, and poorer taste values in comparison to Nip(ALK a ) grains. Taken together, this work provides novel insights underlying the allelic variation of the ALK gene in rice.

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Hybrid rice technology has been used for more than 50 years, and eating and cooking quality (ECQ) has been a major focus throughout this period. Waxy (Wx) and alkaline denaturation (ALK) genes have received attention owing to their pivotal roles in determining rice characteristics. However, despite significant effort, the ECQ of restorer lines (RLs) has changed very little. By contrast, obvious changes have been seen in inbred rice varieties (IRVs), and the ECQ of IRVs is influenced by Wx, which reduces the proportion of Wxa and increases the proportion of Wxb, leading to a decrease in amylose content (AC) and an increase in ECQ. Meanwhile, ALK is not selected in the same way. We investigated Wx alleles and AC values of sterile lines of female parents with the main mating combinations in widely used areas. The results show that almost all sterile lines were Wxa-type with a high AC, which may explain the low ECQ of hybrid rice. Analysis of hybrid rice varieties and RLs in the last 5 years revealed serious homogenisation among hybrid rice varieties.

Rice grain quality is a complex trait that includes processing, appearance, eating, cooking, and nutrition components. The amylose content (AC) in the rice endosperm affects the eating and cooking quality along with the appearance of milled rice. In this study, four indica rice varieties with different ACs were used to study the factors affecting endosperm transparency along with the physical and chemical characteristics and eating quality of translucent endosperm varieties. Endosperm transparency was positively correlated with water content and negatively correlated with the cumulative area of cavities within starch granules. The indica landrace 28Zhan had a translucent endosperm and exhibited good taste. Based on starch fine structure analysis, long-chain amylopectin and the B2 chain of amylopectin might be major contributors to the good taste and relatively slow digestion of this landrace.

Folate deficiency is a global health problem. Biofortification has been considered a cost-effective means to tackle this problem. Here, we describe the genetic cloning and functional identification of a previously uncharacterised plant protein, designated as CTM, which functions as an enzyme in folate metabolism. Plant CTMs are capable of catalysing 5-methyl-tetrahydrofolate to MeFox, a pyrazino-s-triazine derivative of 4α-hydroxy-5-methyl-tetrahydrofolate. The natural asparagine-to-glycine substitution caused by an A-to-G single nucleotide variation in maize CTM enhances its enzymatic activity, as demonstrated by in vitro enzymatic assays and in silico analyses using a maize CTM structure model based on a monomeric sorghum CTM crystal. Loss of the CTM function led to accumulation of 5-methyl-tetrahydrofolate, and overexpression of the maize CTM carrying the G-allele boosted the metabolic flow towards MeFox, and showed no negative impacts on plant growth. Our results suggest that CTM, which has evolved 5-methyl-tetrahydrofolate-to-MeFox converting activity in plants, could be valuable for developing folate-biofortified crops to provide an alternative to the challenge presented by the global folate deficiency.