Skip to main content
SpringerLink
Log in

Pasting properties, grain-filling characteristics and allelic variation linked to the grain quality in diverse rice

  • Published:
Euphytica Aims and scope Submit manuscript

Abstract

Physical appearance and eating and cooking qualities (ECQ) encompassed in rice quality traits have pivotal roles in the new varieties approved, dictating market value. In this regard, it was increasingly important to evaluate various physiological mechanisms, physicochemical properties and the genetic basis involved in controlling grain quality. The investigation in this study showed a large variation in the phenotypic diversity of grain appearance and ECQ among 48 rice accessions. A significant correlation was observed between RVA-pasting properties and multiple grain-quality properties, and attributes of Setback (SB) and consistency (Cons) service as the primary keys in starch pasting. Grain-filling characteristics were surveyed and the principal differences of the trends of rice grain filling were found. The filling rate and duration exhibited significant influence on grain quality. Significant marker-trait association for grain shape, chalkiness and ECQ were explored integrally, proving optional valuable loci can be used for alleles pyramiding. Three SNP markers, GBSSI-G/T, GBSSI-4-IF and SSIIa-GC/TT, can straightforwardly be used for polygenic pyramiding by carrying alleles of T/T, C/C and TT/TT, satisfying for genotype selection for ECQ properties of low-AC, high-GC, and low-GT.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

Abbreviations

AC:

Amylose content

AS:

Area size of grain

ASV:

Alkali spreading value

CS:

Circularity

DEC:

Degree of endosperm chalkiness

GC:

Gel consistency

GL:

Grain length

GT:

Gelatinization temperature

GW:

Grain width

KGW:

1000-grain weight

LWR:

Grain length to width ratio

MAS:

Marker assisted selection

PL:

Perimeter length of grain

PGWC:

Percentage of grain with chalkiness

References

  • Anacleto R, Cuevas RP, Jimenez R, Llorente C, Nissila E, Henry R, Sreenivasulu N (2015) Prospects of breeding high-quality rice using post-genomic tools. Theor Appl Genet 128:1449–1466

    Article  PubMed  Google Scholar 

  • Anand D, Baunthiyal M, Krishnan SG, Singh NK, Prabhu KV, Singh AK (2015) Novel InDel variation in GS3 locus and development of InDel based marker for marker assisted breeding of short grain aromatic rices. J Plant Biochem Biotechnol 24:120–127

    Article  CAS  Google Scholar 

  • Asante MD, Offei SK, Gracen V, Adu-Dapaah H, Danquah EY, Bryant R, Mcclung A (2013) Starch physicochemical properties of rice accessions and their association with molecular markers. Starch-Stärke 65:1022–1028

    Article  CAS  Google Scholar 

  • Bao J-S (2008) Accurate measurement of pasting temperature by the rapid visco-analyser: a case study using rice flour. Rice Sci 15:69–72

    Article  Google Scholar 

  • Bao JS, Corke H, Sun M (2006) Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.). Theor Appl Genet 113:1171–1183

    Article  CAS  PubMed  Google Scholar 

  • Bian J, Li C, He H, Shi H, Yan S (2014) Identification and analysis of QTLs for grain quality traits in rice using an introgression lines population. Euphytica 195:83–93

    Article  Google Scholar 

  • Biselli C, Cavalluzzo D, Perrini R, Gianinetti A, Bagnaresi P, Urso S, Orasen G, Desiderio F, Lupotto E, Cattivelli L, Valè G (2014) Improvement of marker-based predictability of apparent amylose content in japonica rice through GBSSI allele mining. Rice 7(1):1–18

    Article  PubMed  PubMed Central  Google Scholar 

  • Calingacion M, Laborte A, Nelson A, Resurreccion A, Concepcion JC, Daygon VD, Mumm R, Reinke R, Dipti S, Bassinello PZ, Manful J, Sophany S, Lara KC, Bao J, Xie L, Loaiza K, El-hissewy A, Gayin J, Sharma N, Rajeswari S, Manonmani S, Rani NS, Kota S, Indrasari SD, Habibi F, Hosseini M, Tavasoli F, Suzuki K, Umemoto T, Boualaphanh C, Lee HH, Hung YP, Ramli A, Aung PP, Ahmad R, Wattoo JI, Bandonill E, Romero M, Brites CM, Hafeel R, Lur H-S, Cheaupun K, Jongdee S, Blanco P, Bryant R, Thi Lang N, Hall RD, Fitzgerald M (2014) Diversity of global rice markets and the science required for consumer-targeted rice breeding. PLoS ONE 9:e85106

    Article  PubMed  PubMed Central  Google Scholar 

  • Cuevas RP, Pede VO, McKinley J, Velarde O, Demont M (2016) Rice grain quality and consumer preferences: a case study of two rural towns in the philippines. PLoS ONE 11:e0150345

    Article  PubMed  PubMed Central  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Feng H, Wang S-J, Gao Z-N, Zhao J-Z, Zhai X-R (2011) Analysis on grain filling characteristics and yield properties with different rowed barley. Acta Agric Zhejiangensis 1:6

    Google Scholar 

  • Fujita K, Coronel VP, Yoshida S (1984) Grain-filling characteristics of rice varities (oryza sativa L.) differing in grain size under controlled environmental conditions. Soil Sci Plant Nutr 30:445–454

    Article  Google Scholar 

  • Guo L, Zhao H, Wang J, Liu H, Zheng H, Sun J, Yang L, Sha H, Zou D (2016) Dissection of QTL alleles for blast resistance based on linkage and linkage disequilibrium mapping in japonica, rice seedlings. Australas Plant Pathol 45:1–10

    Article  Google Scholar 

  • Hsu YC, Tseng MC, Wu YP, Lin MY, Wei FJ, Hwu KK, Hsing YI, Lin YR (2014) Genetic factors responsible for eating and cooking qualities of rice grains in a recombinant inbred population of an inter-subspecific cross. Mol Breed 34:655–673

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang R, Jiang L, Zheng J, Wang T, Wang H, Huang Y, Hong Z (2013) Genetic bases of rice grain shape: so many genes, so little known. Trends Plant Sci 18:218–226

    Article  CAS  PubMed  Google Scholar 

  • Kadirvel P, Senthilvel S, Geethanjali S, Sujatha M, Varaprasad KS (2015) Genetic markers, trait mapping and marker-assisted selection in plant breeding. In: Bahadur B, Venkat Rajam M, Sahijram L, Krishnamurthy VK (eds) Plant biology and biotechnology. Plant genomics and biotechnology: volume II: Springer, New Delhi, pp 65–88

    Chapter  Google Scholar 

  • Khan Z, Singh T, Hussain JI, Obaid AY, Al-Thabaiti SA, El-Mossalamy EH (2013) Starch-directed green synthesis, characterization and morphology of silver nanoparticles. Colloids Surf B 102:578–584

    Article  CAS  Google Scholar 

  • Kharabian-Masouleh A, Waters DLE, Reinke RF, Ward R, Henry RJ (2012) SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Sci Rep 2:557

    Article  PubMed  PubMed Central  Google Scholar 

  • Kong XL, Sun X, Xu FF, Umemoto T, Chen H, Bao JS (2014) Morphological and physicochemical properties of two starch mutants induced from a high amylose indica rice by gamma irradiation. Starch-Starke 66:157–165

    Article  CAS  Google Scholar 

  • Lee GA, Koh HJ, Chung HK, Dixit A, Chung JW, Ma KH, Lee SY, Lee JR, Lee GS, Gwag JG, Kim TS, Park YJ (2009) Development of SNP-based CAPS and dCAPS markers in eight different genes involved in starch biosynthesis in rice. Mol Breed 24:93–101

    Article  CAS  Google Scholar 

  • Lee CM, Park J, Kim B, Seo J, Lee G, Jang S, Koh HJ (2015) Influence of multi-gene allele combinations on grain size of rice and development of a regression equation model to predict grain parameters. Rice 8:33

    Article  PubMed  PubMed Central  Google Scholar 

  • Leng YJ, Xue DW, Yang YL, Hu SK, Su Y, Huang LC, Wang L, Zheng TT, Zhang GH, Hu J, Gao ZY, Guo LB, Qian Q, Zeng DL (2014) Mapping of QTLs for eating and cooking quality-related traits in rice (Oryza sativa L.). Euphytica 197:99–108

    Article  Google Scholar 

  • Lestari P, Jiang WZ, Chu SH, Reflinur Sutrisno, Kusbiantoro B, Kim B, Piao R, Cho YC, Luo ZX, Chin JH, Koh HJ (2015) DNA markers for eating quality of indica rice in Indonesia. Plant Breed 134:40–48

    Article  Google Scholar 

  • Liu KJ, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129

    Article  CAS  PubMed  Google Scholar 

  • Mo YJ, Jeung JU, Shin WC, Kim KY, Ye CR, Redona ED, Kim BK (2014) Effects of allelic variations in starch synthesis-related genes on grain quality traits of Korean nonglutinous rice varieties under different temperature conditions. Breed Sci 64:164–175

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oliveira Borba TC, Brondani RP, Breseghello F, Coelho AS, Mendonca JA, Rangel PH, Brondani C (2010) Association mapping for yield and grain quality traits in rice (Oryza sativa L.). Genet Mol Biol 33:515–524

    Article  PubMed  PubMed Central  Google Scholar 

  • Phing Lau WC, Latif MA, YR M, Ismail MR, Puteh A (2016) Advances to improve the eating and cooking qualities of rice by marker-assisted breeding. Crit Rev Biotechnol 36:87–98

    Article  PubMed  Google Scholar 

  • Richards FJ (1959) A flexible growth function for empirical use. J Exp Bot 10:290–301

    Article  Google Scholar 

  • Su Y, Rao YC, Hu SK, Yang YL, Gao ZY, Zhang GH, Liu J, Hu J, Yan MX, Dong GJ, Zhu L, Guo LB, Qian Q, Zeng DL (2011) Map-based cloning proves qGC-6, a major QTL for gel consistency of japonica/indica cross, responds by waxy in rice (Oryza sativa L.). Theor Appl Genet 123:859–867

    Article  PubMed  Google Scholar 

  • Tanabata T, Shibaya T, Hori K, Ebana K, Yano M (2012) SmartGrain: high-throughput phenotyping software for measuring seed shape through image analysis. Plant Physiol 160:1871–1880

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tian ZX, Qian Q, Liu QQ, Yan MX, Liu XF, Yan CJ, Liu GF, Gao ZY, Tang SZ, Zeng DL, Wang YH, Yu JM, Gu MH, Li JY (2009) Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci USA 106:21760–21765

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tran DS, Tran TTH, Nguyen TLH, Ha ML, Dinh BY, Kumamaru T, Satoh H (2013) Variation on starch properties and the relationship to single nucleotide polymorphism in SSIIa in waxy rice collected from central of Vietnam. J Fac Agric Kyushu Univ 58:247–252

    CAS  Google Scholar 

  • Tuaño APP, Regalado MJC, Juliano BO (2016) Grain quality of rice in selected retail stores and supermarkets in the Philippines. J Philipp Sci Techol 9:15–22

    Google Scholar 

  • Wang E, Wang J, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40:1370–1374

    Article  CAS  PubMed  Google Scholar 

  • Wang ZQ, Xu YJ, Wang JC, Yang JC, Zhang JH (2012) Polyamine and ethylene interactions in grain filling of superior and inferior spikelets of rice. Plant Growth Regul 66:215–228

    Article  CAS  Google Scholar 

  • Wang L, Deng F, Ren WJ, Yang WY (2013) Effects of shading on starch pasting characteristics of indica hybrid rice (Oryza sativa L.). PLoS ONE 8:e68220

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang L, Lu Q, Wen X, Lu C (2015) Enhanced sucrose loading improves rice yield by increasing grain size. Plant Physiol 169:2848–2862

    CAS  PubMed  PubMed Central  Google Scholar 

  • Xu J, Jiang J, Dong X, Ali J, Mou T (2012) Introgression of bacterial blight (BB) resistance genes Xa7 and Xa21 into popular restorer line and their hybrids by molecular marker-assisted backcross (MABC) selection scheme. Afr J Biotechnol 11:8225–8233

    CAS  Google Scholar 

  • Xu FF, Zhang G, Tong C, Sun X, Corke H, Sun M, Bao JS (2013) Association mapping of starch physicochemical properties with starch biosynthesizing genes in waxy rice (Oryza sativa L.). J Agric Food Chem 61:10110–10117

    Article  CAS  PubMed  Google Scholar 

  • Yang JC, Zhang JH (2010) Grain-filling problem in ‘super’ rice. J Exp Bot 61:1–4

    Article  CAS  PubMed  Google Scholar 

  • Yang F, Chen YL, Tong C, Huang Y, Xu FF, Li KH, Corke H, Sun M, Bao JS (2014) Association mapping of starch physicochemical properties with starch synthesis-related gene markers in nonwaxy rice (Oryza sativa L.). Mol Breed 34:1747–1763

    Article  CAS  Google Scholar 

  • Zhao XQ, Zhou LJ, Ponce K, Ye GY (2015) The usefulness of known genes/QTLs for grain quality traits in an indica population of diverse breeding lines tested using association analysis. Rice 8:1–13

    Article  Google Scholar 

  • Zhao XQ, Daygon VD, McNally KL, Hamilton RS, Xie FM, Reinke RF, Fitzgerald MA (2016) Identification of stable QTLs causing chalk in rice grains in nine environments. Theor Appl Genet 129:141–153

    Article  CAS  PubMed  Google Scholar 

  • Zheng HL, Wang JG, Zhao HW, Liu HL, SunJ J, Guo LY, Zou DT (2015) Genetic structure, linkage disequilibrium and association mapping of salt tolerance in japonica rice germplasm at the seedling stage. Mol Breed 35:1–16

    Article  Google Scholar 

  • Zhou LJ, Jiang L, Zhai HQ, Wan JM (2009) Current status and strategies for improvement of rice grain chalkiness. Hereditas 31:563–572

    Article  CAS  PubMed  Google Scholar 

  • Zhu Q, Cao X, Luo Y (1988) Growth analysis in the process of grain filling in rice. Acta Agron Sin 14:182–193

    Google Scholar 

Download references

Acknowledgements

Financial support for this research was provided in part by a grant from the National Key Technology Research and Development Program of China (No. 2016YFD0102102), Science and technology project of Guangdong Province (No. 2015B020231011) and the earmarked fund for Modern Agro-industry Technology Research System (No. CARS-01-12).

Authors contribution

T.G. Z.C. and H.W. designed the overall experiment and edited the manuscript. L.C. X.Y. and W.G. did genotyping, phenotyping, data analysis and wrote this manuscript. J.Y. L.W. S.C. Z.G. and J.Z. assisted in data analysis and participated in preparation of the manuscript. All authors read and approved the final manuscript.

Author information

Authors and Affiliations

  1. National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, Guangdong, China

    Likai Chen, Xianchen Yan, Liping Wang, Weiwei Gao, Jing Yang, Siping Chen, Hui Wang, Zhiqiang Chen & Tao Guo

  2. Guangdong Agricultural Technology Extension Station, Guangzhou, 510520, Guangdong, China

    Jiyong Zhou

  3. Jiamusi Rice Research Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154026, Heilongjiang, China

    Zhenhua Guo

Authors
  1. Likai Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xianchen Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Liping Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Weiwei Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jing Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Siping Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Zhenhua Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jiyong Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Hui Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Zhiqiang Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Tao Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Zhiqiang Chen or Tao Guo.

Ethics declarations

Conflict of interest

The authors declare that they have no competing interests.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chen, L., Yan, X., Wang, L. et al. Pasting properties, grain-filling characteristics and allelic variation linked to the grain quality in diverse rice. Euphytica 213, 29 (2017). https://doi.org/10.1007/s10681-016-1811-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10681-016-1811-2

Keywords

Search

Navigation