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 o...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.展开更多
Rice eating and cooking quality(ECQ)is significantly influenced by the physicochemical properties of rice starch.This study integrates whole-genome resequencing,transcriptomic data,and phenotypic analysis to identify t...Rice eating and cooking quality(ECQ)is significantly influenced by the physicochemical properties of rice starch.This study integrates whole-genome resequencing,transcriptomic data,and phenotypic analysis to identify the genetic factors that regulate transcript expression levels and contribute to phenotypic variation in rice ECQ traits.A TWAS(transcriptome-wide association study)identified 285 transcripts linked to 6 ECQ traits.Genome-wide mapping of these transcripts revealed 21747 local eQTLs(expression quantitative trait loci)and 45158 distal eQTLs.TWAS and eQTL analysis detected several known and novel genes,including starch synthesis-related genes,heat shock proteins,transcription factors,genes related to ATP accumulation,and UDP-glucosyltransferases,showcasing the complex genetic regulation of rice ECQ.WGCNA(weighted gene co-expression network analysis)uncovered key co-expression networks,including a module that links alpha-globulin1(GLB1)tostarchandsucrosemetabolism.GeneticdiversityanalysisoftheGLB1geneacrossaKorean rice collection identified 26 haplotypes,with indica and aus forming 7 and 3 haplotypes,respectively,which showedsignificantphenotypiceffectsonECQtraits.CRISPR-Cas9-createdknockoutlinesvalidatedthesefind-ings,demonstrating that loss of GLB1 function caused significant changes in seed storage proteins,reduced amylose content,altered starch granules,and modified pasting properties without affecting plant phenotypes.By integrating TWAS,eQTL mapping,haplotype analysis,gene expression networks,and CRISPR validation,this study establishes GLB1 as a regulator of ECQ,linking starch biosynthesis and protein accumulation path-ways.This transcriptogenomic convergence approach provides novel insights into the genetic regulation of ECQ in rice,demonstrating its effectiveness for characterizing complex traits and enabling precision breeding.展开更多
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 iden...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.展开更多
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 f...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.展开更多
基金This research was financially supported by the National Key Research and Development Program of China(2017YFD0100300,2016YFD0101801)the National S&T Major Project,China(2016ZX08001006)+1 种基金the National Nature Science Foundation of China(31871597)the Zhejiang Science and Technology Projects,China(L GN18C130006).
文摘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.
基金supported by National Research Foundation of Korea(NRF)grants funded by the Korean government(MSIT)(NRF-2022R1A 4A1030348 and NRF-2023R1A2C1004432)the Development of Next-Generation Crop Breeding Technologies(RS-2024-00322378)Rural Development Administration,Republic of Korea.
文摘Rice eating and cooking quality(ECQ)is significantly influenced by the physicochemical properties of rice starch.This study integrates whole-genome resequencing,transcriptomic data,and phenotypic analysis to identify the genetic factors that regulate transcript expression levels and contribute to phenotypic variation in rice ECQ traits.A TWAS(transcriptome-wide association study)identified 285 transcripts linked to 6 ECQ traits.Genome-wide mapping of these transcripts revealed 21747 local eQTLs(expression quantitative trait loci)and 45158 distal eQTLs.TWAS and eQTL analysis detected several known and novel genes,including starch synthesis-related genes,heat shock proteins,transcription factors,genes related to ATP accumulation,and UDP-glucosyltransferases,showcasing the complex genetic regulation of rice ECQ.WGCNA(weighted gene co-expression network analysis)uncovered key co-expression networks,including a module that links alpha-globulin1(GLB1)tostarchandsucrosemetabolism.GeneticdiversityanalysisoftheGLB1geneacrossaKorean rice collection identified 26 haplotypes,with indica and aus forming 7 and 3 haplotypes,respectively,which showedsignificantphenotypiceffectsonECQtraits.CRISPR-Cas9-createdknockoutlinesvalidatedthesefind-ings,demonstrating that loss of GLB1 function caused significant changes in seed storage proteins,reduced amylose content,altered starch granules,and modified pasting properties without affecting plant phenotypes.By integrating TWAS,eQTL mapping,haplotype analysis,gene expression networks,and CRISPR validation,this study establishes GLB1 as a regulator of ECQ,linking starch biosynthesis and protein accumulation path-ways.This transcriptogenomic convergence approach provides novel insights into the genetic regulation of ECQ in rice,demonstrating its effectiveness for characterizing complex traits and enabling precision breeding.
基金This work was supported by the Ministry of Science and Technology of China(2016YFD0100501)National Natural Science Foundation of China(31825019,31901517,and U19A2032)the Programs from Jiangsu Province Government(BE2018357,19KJA560006 and PAPD)。
文摘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.
基金supported by funding from the National Natural Science Foundation of China(31801016)the Agricultural Variety Improvement Project of Shandong Province(2019LZGC015)。
文摘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.
