A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency

In rice(Oryza sativa), amylose content(AC) is the major factor that determines eating and cooking quality(ECQ). The diversity in AC is largely attributed to natural allelic variation at the Waxy(Wx)locus. Here we identified a rare Wx allele, Wx^(mw) ,which combines a favorable AC, improved ECQ and grain transparency. Based on a phylogenetic analysis of Wx genomic sequences from 370 rice accessions, we speculated that Wx^(mw) may have derived from recombination between two important natural Wx alleles, Wx^(in) and Wx^(b). We validated the effects of Wx^(mw) on rice grain quality using both transgenic lines and near-isogenic lines(NILs). When introgressed into the japonica Nipponbare(NIP) background, Wx^(mw) resulted in a moderate AC that was intermediate between that of NILs carrying the Wx^(b)allele and NILs with the Wx^(mp) allele. Notably, mature grains of NILs fixed for Wx^(mw) had an improved transparent endosperm relative to soft rice. Further, we introduced Wx^(mw) into a high-yielding japonica cultivar via molecular marker-assisted selection: the introgressed lines exhibited clear improvements in ECQ and endosperm transparency. Our results suggest that Wx^(mw) is a promising allele to improve grain quality, especially ECQ and grain transparency of high-yielding japonica cultivars, in rice breeding programs.

Rapid improvement of rice eating and cooking quality through gene editing toward glutelin as target

Rice eating and cooking quality(ECQ)is a major concern of breeders and consumers,determining market competitiveness worldwide.Rice grain protein content(GPC)is negatively related to ECQ,making it possible to improve ECQ by manipulating GPC.However,GPC is genetically complex and sensitive to environmental conditions;therefore,little progress has been made in traditional breeding for ECQ.Here,we report that CRISPR/Cas9-mediated knockout of genes encoding the grain storage protein glutelin rapidly produced lines with downregulated GPC and improved ECQ.Our finding provides a new strategy for improving rice ECQ.

Comparison of grain yield and quality of different types of japonica rice cultivars in the northern Jiangsu plain,China

In recent years,an increasing number of different types of japonica rice cultivars have been released in the southern rice region of China.The grain yield and quality of these new cultivars showed significant differences in large scale planting.However,the causes of the differences remain little known.Therefore,three typical types of japonica rice cultivars were used in this study to investigate their grain yield and quality.A scanning calorimeter(DSC),X-ray powder diffractometer(XRD),rapid viscosity analyzer(RVA)and taste analyzer were used to evaluate the cooking and eating properties.The results showed that the yield of non-soft hybrid japonica rice cultivars was significantly higher than that of non-soft inbred japonica rice cultivars and soft inbred japonica rice cultivars.Soft inbred japonica rice cultivars had a low amylose content and moderate protein content,which are the main reasons for the superior cooking and eating quality.In addition,the relative crystallinity of soft inbred japonica rice cultivars was significantly higher than that of non-soft inbred and non-soft hybrid japonica rice cultivars,which is considered the major factor resulting in higher transition temperature and gelatinization enthalpy(ΔH_(gel)).Non-soft hybrid japonica rice cultivars had a higher number of large starch granules than soft inbred and non-soft inbred japonica rice cultivars.The setback value(SB)and breakdown value(BD),indirectly reflecting the cooking and eating quality of the three types of japonica rice cultivars,also confirmed that soft inbred japonica rice cultivars with a low SB value and a high BD value had better palatability than the other two types.This study provides guidance for future plantation of different types of japonica rice cultivars in large rice-producing areas.

Analysis of Quantitative Trait Loci for Starch Properties of Rice Based on an RIL Population

Rice (Oryza sativa L.) eating and cooking quality is mainly influenced by its starch properties. Mapping quantitative trait loci (QTL) for starch properties not only helps us understand their genetic basis leading to acceleration of quality improvement, but also helps us find possible genes participating in the synthesis of starch. A recombinant inbred line (RIL) population consisting of 107 lines, derived from an indica (Zaiyeqing 8, ZYQ 8) and a japonica (Jingxi 17, JX 17) rice, was used to investigate the genetic factors affecting starch quality parameters, such as apparent amylose content (AAC), gel consistency (GC), starch pasting viscosity parameters, gel textural properties, gelatinization temperature (GT) and starch retrogradation properties. A total of 44 QTLs covered chromosomes 2-6, 8, 9 and 11 were detected for the 22 traits, with at least one QTL and as many as four QTLs for each individual trait. The results indicated that two major genes were responsible for most starch property traits. The Wx gene that encodes granule bound starch synthase on chromosome 6 was significant for AAC, GC, starch pasting viscosity parameters, gel textural properties and starch retrogradation properties. The alk gene linked with Wx on chromosome 6 was significant for starch gelatinization temperature characteristics. All other QTLs were minor genes. One QTL on chromosome 9 flanked by RZ404 and G295 was significant for gel hardness (HD), gumminess (GUM), chewiness (CHEW), peak temperature of retrogradated starch (RTp), and percentage retrogradation (R%) and all these traits were not tested before.

Mapping quantitative trait loci associated with starch paste viscosity attributes by using double haploid populations of rice (Oryza sativa L.)

The paste viscosity attributes of starch,measured by rapid visco analyzer(RVA),are important factors for the evaluation of the cooking and eating qualities of rice in breeding programs.To determine the genetic roots of the paste viscosity attributes of rice grains,quantitative trait loci(QTLs)associated with the paste viscosity attributes were mapped,using a double haploid(DH)population derived from Zhongjiazao 17(YK17),a super rice variety,crossed with D50,a tropic japonica variety.Fifty-four QTLs,for seven parameters of the RVA profiles,were identified in three planting seasons.The 54 QTLs were located on all of the 12 chromosomes,with a single QTL explaining 5.99 to 47.11%of phenotypic variation.From the QTLs identified,four were repeatedly detected under three environmental conditions and the other four QTLs were repeated under two environments.Most of the QTLs detected for peak viscosity(PKV),trough viscosity(TV),cool paste viscosity(CPV),breakdown viscosity(BDV),setback viscosity(SBV),and peak time(PeT)were located in the interval of RM 6775-RM 3805 under all three environmental conditions,with the exception of pasting temperature(PaT).For digenic interactions,eight QTLs with six traits were identified for additivexenvironment interactions in all three planting environments.The epistatic interactions were estimated only for PKV,SBV and PaT.The present study will facilitate further understanding of the genetic architecture of eating and cooking quality(ECQ)in the rice quality improvement program.

Post-genomics revolution in the design of premiumquality rice in a high-yieldingbackground to meet consumer demands in the 21st century

The eating and cooking quality(ECQ)of rice is critical for determining its economic value in the marketplace and promoting consumer acceptance.It has therefore been of paramount importance in rice breeding programs.Here,we highlight advances in genetic studies of ECQ and discuss prospects for further enhancement of ECQ in rice.Innovations in gene-and genome-editing techniques have enabled improvements in rice ECQ.Significant genes and quantitative trait loci(QTLs)have been shown to regulate starch composition,thereby affecting amylose content and thermal and pasting properties.A limited number of genes/QTLs have been identified for other ECQ properties such as protein content and aroma.Marker-assisted breeding has identified rare alleles in diverse genetic resources that are associated with superior ECQ properties.The post-genomics-driven information summarized in this review is relevant for augmenting current breeding strategies to meet consumer preferences and growing population demands.

Novel Wx alleles generated by base editing for improvement of rice grain quality

Amylose content(AC),which is regulated by the Waxy(Wx)gene,is a major indicator of eating and cooking quality(ECQ)in rice(Oryza sativa).Thus far,only a limited number of mutations in the N-terminal domain of Wx were found to have a major impact on the AC of rice grains and no mutations with such effects were reported for other regions of the Wx protein.Here,nucleotide substitutions in the middle region of Wx were generated by adenine and cytosine base editors.The nucleotide substitutions led to changes in 15 amino acid residues of Wx,and a series of novel Wx alleles with ACs of 0.3%-29.43%(wild type with AC of 19.87%)were obtained.Importantly,the waxy~(abe2)allele showed a"soft rice"AC,improved ECQ,favorable appearance,and no undesirable agronomic traits.The transgenes were removed from the waxy~(abe2)progeny,generating a promising breeding material for improving rice grain quality.