No abstract

The Wx gene encodes a granule-bound starch synthase (GBSS) and plays a key role in determining rice eating and cooking qualities (ECQs). SSIII-2 (SSIIIa), a member of the soluble starch synthases, is responsible for the synthesis of long chains of amylopectin. To investigate the effects of Wx and its interaction with SSIII-2 on grain ECQs, a population from a hybrid combination was established as a research material. The genotypes of SSIII-2 and the single nucleotide polymorphisms (SNPs) on intron1, exon6, and exon10 of Wx, and the physicochemical indicators and rapid visco analyzer (RVA) profile characteristics were analyzed. The results revealed various effects of SSIII-2 on rice quality under different backgrounds of Wx alleles. There was no obvious difference between different SSIII-2 alleles under the same background of Wxa, whereas there was a significant diversity under the same background of Wxb. Wxa had a dominant epistasis to SSIII-2 because the effect of SSIII-2 was masked by the massive synthesis of GBSS under Wxa. The apparent amylose content (AAC) was mainly controlled by the In1G/T SNP, and rice gel consistency (GC) was regulated by the Ex10C/T SNP. The combined effects of three SNPs had a significant influence on all ECQs and RVA profile parameters, except for gelatinization temperature. In1T-Ex6A-Ex10C and In1T-Ex6A-Ex10T were classified as being low AAC type. TT-AA-CC and TT-AA-TT had a low AAC and a soft GC. The combined effects of different SNPs of Wx are very important for rice quality breeding.

Glutinous rice (Oryza sativa L.) quality includes thermal properties, retrogradation and pasting viscosity properties, and so on, which have little or no amylose. However, the genetic network regulation of different quality indices has not been systematically studied. The aim was to investigate the relationship between starch synthesis-related genes (SSRGs) and the physicochemical properties of glutinous rice by targeted-gene association analysis (TGAS). The genotypes of 17 SSRGs were analyzed using 46 gene-specific molecular markers in 63 glutinous rice accessions. TGAS and gene interactions analysis indicated that soluble starch synthase (SS) IIa, SSI, starch branching enzyme (BE) IIa, and pullulanase (PUL) had significant genetic effects on glutinous rice quality. SSI and SSIIa were the major genes that regulated thermal properties and retrogradation properties (RP). PUL was central in the regulation of gel consistency (GC), and it participated in the regulation of pasting viscosity parameters (PVP) except for the pasting time and the pasting temperature. BEIIb, ISA1, SSIVb, BEIIa, SSIVa, and their interactions with SSIIa regulated gelatinization temperature (GT) and PVP. The starch properties of glutinous rice are mainly controlled by SSIIa, SSI, PUL, and their interactions, but SSIIa is central among them. These findings indicate that starch properties in glutinous rice have a complex genetic system. It provides crucial information for promoting glutinous rice quality.

Background Rice amylose content and amylopectin structure corporately determine rice eating and cooking qualities (ECQs). Soluble starch synthase ( SS ) IV-2 is a member of the soluble starch synthesis gene family but with unknown effects on ECQs. Results In this study, three populations derived from a cross of two parents who possess the same major genes of starch bio-synthesis were employed to investigate the influence of SSIV-2 and its combined effects with ADPglucose pyrophorylase large unit ( AGPlar ) and Pullulanase ( PUL ) on ECQs. The results illustrated that the polymorphism of SSIV-2 alleles significantly affected gel consistency (GC), gelatinization temperature (GT), percent of retrogradation (PR) and three crucial rapid viscosity analysis (RVA) profile parameters: peak viscosity (PKV), breakdown viscosity (BDV) and setback viscosity (SBV). And SSIV-2 allele derived from CG173R had better quality traits with lower GT, SBV and PR. Moreover, its interaction with AGPlar was responsible for the variations of GC, apparent amylose content (AAC), GT, PR and all RVA parameters except for pasting temperature (PaT) and peak time (PeT), in terms of GC, PKV and CSV, AGPlar derived from CG173R had an epistatic effect on SSIV-2 ; additionally, interaction of SSIV-2 and PUL mainly affected GC, AAC, PKV, CPV, CSV and SBV. I-C and C-1 (I, allele of AGPlar from Guangzhan 63S; C, allele of SSIV-2 from CG173R; 1, allele of PUL from Guangzhan 63S) combinations had better ECQs. Conclusions SSIV-2 alleles significantly affect rice quality, especially the parameters relevant to gelatinized and thermal characteristics of starch (GC, PR, GT, PKV, BDV and SBV) under the same major genes ( Waxy and SSII-3 ) background. It indicates that SSIV-2 functions elongation of starch chain. These findings suggest that the effects of SSIV-2 and its interaction with AGPlar and PUL are vital for rice quality breeding with the same major genes.

BACKGROUND: Soluble starch synthase IIa (ALK, SSII-3) is the major gene regulating gelatinization temperature (GT) and SSII-3 M1 is an effective marker for identifying SSIIa alleles. However, the haplotypes of SSIIa alleles amplified by SSII-3M1 and their allelic effect sunder different Waxy (Wx) background in non-glutinous rice remain unclear. RESULTS: By integrating the genetic background analysis and by the identification of the genotypes of Wx and SSIIa, we found that the SSIIa alleles amplified by SSII-3 M1 were haplotype 1 (G/G/GC, indica-type) and 4 (A/G/TT, japonica-type), which had a significant effect on pasting temperature (PaT), hot paste viscosity (HPV), and the alkali spreading value (ASV). There were significant effects of SSIIa alleles on HPV, cool paste viscosity (CPV), and consistency value with different Wx backgrounds. The apparent amylose content (AAC) of samples significantly affected the accuracy of GT, which was represented by the manually determined pasting temperature (PTm). CONCLUSIONS: The SSIIa alleles amplified by SSII-3 M1 are indica type and japonica type. Different SSIIa haplotypes significantly affect HPV, CPV, PaT, and ASV. GT, PaT, and PTm are mainly affected by SSIIa alleles. The classification of all samples with different haplotypes of SSIIa indicates that their AAC (Wx genotypes) is essentially. The effects of SSIIa alleles are themselves affected by different Wx alleles.

No abstract

Seedling vigor is of vital importance for the initial plant establishment of direct-seeded rice. Here, 166 recombinant inbred lines were employed to assess eight seedling vigor traits over the first 25 days of germination. Significant correlations were found between most traits, and statistical analysis has revealed, for the first time, a linear relationship that uses seedling height and fresh weight to accurately predict the accumulation of dry biomass. Further, a subset of 20 lines, spanning the phenotypic range of the larger population, were genotyped by using 16 simple sequence repeats (SSR) markers known to be associated with seedling vigor traits. Markers RM317 and RM348 linked with significantly different phenotypes, including seedling height and fresh weight. One combination, haplotype II-1 (RM317 (I/II) and RM348 (1/2)), consistently produced superior values for seedling height, root length, and leaf length. The new prediction tool for seedling dry weight, namely the haplotype of RM317 and RM348, will have a wide range of applications in breeding strategies by using markerassisted selection to produce elite lines that optimize genetic composition contributing to seedling vigor.

BackgroundResistant Starch (RS) is a healthy dietary fiber that has functions of regulating diabetes, hypertension and obesity. Previous studies mainly focused on investigating RS in raw rice or cooked rice separately, which may receive different results. ResultsIn this study, ninety-nine lines from a recombinant inbred line (RIL) were selected to investigate the effects of starch synthesis-related genes on the RS content in different process status. RS content in rice will change by different processing ways. Waxy (Wx) played an important role in controlling RS content and Wxa could elevate RS content, and soluble starch synthaseII-3 (SSII-3) had an impact on RS2. Additionally, interaction of Wx and SSII-3 was responsible for variations of RS content in three sample types and RS2. Wx could affect RS in cooked rice and retrograded rice under the same SSII-3 allele. Moreover, the correlation analysis results indicated that RS was closely relative with many indexes of physicochemical properties. ConclusionsWx and SSII-3 could regulate RS content of rice, but SSII-3 especially affected RS2. The findings herein should provide useful information for molecular breeding of rice RS.