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

doi:10.1016/S2095-3119(19)62726-7

摘要/Abstract

Abstract:

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 RM6775–RM3805 under all three environmental conditions, with the exception of pasting temperature (PaT). For digenic interactions, eight QTLs with six traits were identified for additive×environment 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.

Key words: RVA profiles , eating and cooking quality (ECQ) , quantitative trait loci (QTL) , DH population , rice

. [J]. Journal of Integrative Agriculture, 2020, 19(7): 1691-1703.

Tahmina SHAR, SHENG Zhong-hua, Umed ALI, Sajid FIAZ, WEI Xiang-jin, XIE Li-hong, JIAO Gui-ai, Fahad ALI, SHAO Gao-neng, HU Shi-kai, HU Pei-song, TANG Shao-qing. Mapping quantitative trait loci associated with starch paste viscosity attributes by using double haploid populations of rice (Oryza sativa L.)[J]. Journal of Integrative Agriculture, 2020, 19(7): 1691-1703.

参考文献

Bao J S. 2012. Toward understanding the genetic and molecular bases of the eating and cooking qualities of rice. Cereal Foods World, 57, 148–156.
Bao J S, Xia Y W. 1999. Genetic control of the paste viscosity characteristics in indica rice (Oryza sativa L.). Theoretical and Applied Genetics, 98, 1120–1124.
Bao J S, Zheng X W, Xia Y W, He P, Shu Q Y, Lu X, Chen Y, Zhu L H. 2000. QTL mapping for the paste viscosity characteristics in rice (Oryza sativa L.). Theoretical and Applied Genetics, 100, 280–284.
Bergman C J, Bhattacharya K R, Ohtsubo K. 2004. Rice end-use quality analysis. In: RICE: Chemistry and Technology. American Association of Cereal Chemists, St. Paul. pp. 415–472.
Bryant R J, Anders M, McClung A. 2012. Impact of production practices on physicochemical properties of rice grain quality. Journal of the Science of Food and Agriculture, 92, 564–569.
Chen M H, Bergman C, Pinson S, Fjellstrom R. 2008. Waxy gene haplotypes: Associations with apparent amylose content and the effect by the environment in an international rice germplasm collection. Journal of Cereal Science, 47, 536–545.
Chung H J, Liu Q, Lee L, Wei D Z. 2011. Relationship between the structure, physicochemical properties and in vitro digestibility of rice starches with different amylose contents. Food Hydrocoll, 25, 968–975.
Chung W K, Han A, Saleh M, Meullenet J F. 2003. Prediction of long-grain rice texture from pasting properties. BR Wells Arkansas Rice Research Studies, 517, 355–361.
Hu P S, Zhai H Q, Tang S Q, Wang J M. 2004. Rapid evaluation of rice cooking and palatability quality by RVA profile. Acta Agronomica Sinica, 30, 519–524. (in Chinese)
Jiang H W, Dian W M, Liu F Y, Wu P. 2004. Molecular cloning and expression analysis of three genes encoding starch synthase II in rice. Planta, 218, 1062–1070.
Jiang H W, Dian W M, Wu P. 2003. Effect of high temperature on fine structure of amylopectin in rice endosperm by reducing the activity of the starch branching enzyme. Phytochemistry, 63, 53–59.
Jiao G, Wei X, Tang S, Sheng Z, Xie L, Shao G, Fiaz S, Hu P, Xu Q. 2018. Stirring affects starch granule morphology and the functional properties of rice flour. Starch/Stärke, 70, 3–4.
Jin J, Xu D Y, Cai Y X. 2004. Effect of N-fertilizer on main quality characters of rice and RVA profile parameters. Acta Agronomica Sinica, 30, 154–158. (in Chinese)
Jin Z X, Qian C R, Yang J, Liu H Y, Jin X Y. 2005. Effect of temperature at grain filling stage on activities of key enzymes related to starch synthesis and grain quality of rice. Rice Science, 12, 261–266.
Kang M Y, Rico C W, Kim C E, Lee S C. 2011. Physicochemical properties and eating qualities of milled rice from different Korean elite rice varieties. International Journal of Food Properties, 14, 640–653.
Kesarwani A, Chiang P Y, Chen S S. 2016. Rapid visco analyzer measurements of japonica rice cultivars to study interrelationship between pasting properties and farming system. International Journal of Agronomy, 2, doi: 10.1155/2016/3595326
Kharabian-Masouleh A, Daniel L E W, Russell F R, Rachelle W, Robert J H. 2012. SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Scientific Reports, 2, 557.
Kuo B J, Hong M C, Thseng F S. 2001. The relationship between the amylographic characteristics and eating quality of japonica rice in Taiwan. Plant Production Science, 4, 112–117.
Larkin P D, Park W D. 2003. Association of waxy gene single nucleotide polymorphisms with starch characteristics in rice (Oryza sativa L.). Molecular Breeding, 12, 335–339.
Li J J, Zhang W, Wu H, Guo T, Liu X, Wan X, Jin J S, Hanh T T T, Thoa N T N, Chen M J, Liu S, Chen L M, Liu X, Wang J K, Zhai H, Wan J M. 2011. Fine mapping of stable QTLs related to eating quality in rice (Oryza sativa L.) by CSSLs harboring small target chromosomal segments. Breeding Science, 61, 338–346.
Limpisut P, Jindal V K. 2002. Comparison of rice flour pasting properties using brabender viscoamylograph and rapid visco analyser for evaluating cooked rice texture. Starch/Stärke, 54, 350–357.
Liu X, Wan X, Ma X, Wan J. 2011. Dissecting the genetic basis for the effect of rice chalkiness, amylose content, protein content, and rapid viscosity analyzer pro?le characteristics on the eating quality of cooked rice using the chromosome seg-ment substitution line population across eight environments. Genome, 54, 64–80.
Lur H S, Hsu C L, Wu C W, Lee C Y, Lao C L, Wu Y C, Chang S J, Wang C Y, Kondo M. 2009. Changes in temperature cultivation timing and grain quality of rice in Taiwan in recent years. Crop Environment & Bioinformatics, 6, 175–182.
Van Ooijen J W. 2006. Join Map 4, Software for the Calculation of Genetic Linkage Maps in Experimental Populations. Wageningen, The Netherlands.
Pang Y, Ali J, Wang X, Franje N J, Revilleza J E, Xu J, Li Z. 2016. Relationship of rice train amylose, gelatinization temperatureand pasting propertiesfor breeding better eating and cooking quality of rice varieties. PLoS ONE, 11, e0168483.
Ponce K S, Ye G, Zhao X. 2018. QTL identification for cooking and eating quality in indica rice using multi-parent advanced generation intercross (MAGIC) population. Frontiers in Plant Science, 9, 1–9.
Raina C S, Singh S, Bawa A S, Saxena D C. 2007. A comparative study of Indian rice starches using different modification model solutions. Food Science and Technology, 40, 885–892.
Ryoo N, Yu C, Park C S, Baik M Y, Park I M, Cho M H, Bhoo S H, An G H, Hahn T R, Seong J. 2007. Knockout of a starch synthase gene OsSSIIIa/Flo5 causes white-core floury endosperm in rice (Oryza sativa L.). Plant Cell Reprorts, 26, 1083–1095.
Shafie B, Cheng S C, Lee H H, Yiu P H. 2016. Characterization and classification of whole-grain rice based on rapid visco analyzer (RVA) pasting profile. International Food Research Journal, 23, 2138–2143.
Shen S Q, Zhuang J Y, Shu Q Y, Bao J S, Wu D X, Xia Y W. 2005. Analysis of QTLs with main, epistasis and G×E interaction effects of starch paste viscosity in rice. Acta Agronomica Sinica, 31, 1289–1294. (in Chinese)
Tan Y F, Li J X, Yu S B, Xing Y Z, Xu C G, Zhang Q. 1999. The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid. Shanyou 63. Theoretical Applied Genetics, 99, 642–648.
Tong C, Chen Y, Tang F, Xu F, Huang Y, Chen H, Bao J. 2014. Genetic diversity of amylose content and RVA pasting parameters in 20 rice accessions grown in Hainan China. Food Chemistry, 161, 239–245.
Traore K, McClung A M, Chen M H, Fjellstrom R. 2011. Inheritance of ?our paste viscosity is associated with a rice Waxy gene exon 10 SNP marker. Journal of Cereal Science, 53, 37–44.
Umemoto T, Aoki N, Lin H, Nakamura Y, Inouchi N, Sato Y, Yano M, Hirabayashi H, Maruyama S. 2004. Natural variation in rice starchs ynthase IIa affects enzyme and starch properties. Functional Plant Biology, 31, 671–684.
Umemoto T, Horibata T, Aoki N, Hiratsuka M, Yano M, Inouch N. 2008. Effects of variations in starch synthase on starch properties and eating quality of rice. Plant Production Science, 11, 472–480.
Wan X Y, Wan J M, Su C C, Wang C M, Shen W B, Li J M, Wang H L, Jiang L, Liu S J, Chen L M. 2004. QTL detection for eating quality of cooked rice in a population of chromosome segment substitution lines. Theoretical and Applied Genetics, 110, 71–79.
Wan X Y, Wan J M, Weng J F, Jiang L, Bi J C, Wang C M, Zhai H Q. 2005. Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments. Theoretical and Applied Genetics, 110, 1334–1346.
Wang S. 2007. Windows QTL cartographer 2.5. [2017-05-24]. http://statgen.ncsu.edu/qtlcart/WQTLCart.html
Wang S, Basten C J, Zeng Z B. 2006. Windows QTL Cartographer 2.5 Department of Statistics. North Carolina State University, Raleigh, USA.
Wei K S, Cheng F M, Zhang Q F, Liu K G. 2009. Temperature stress at grain filling stage mediates expression of three isoform genes encoding starch branching enzymes in rice endosperm. Rice Science, 16, 187–193.
Wendy C P L, Mohammad A L, Mohd Y R, Mohd R I, Adam P. 2014. Advances to improve the eating and cooking qualities of rice by marker-assisted breeding. Critical Reviews in Biotechnology, 9, 1549–7801.
Xu F, Sun C, Huang Y, Chen Y, Tong C, Bao J. 2015. QTL mapping for rice grain quality: A strategy to detect more QTLs within sub-populations. Molecular Breeding, 35, 105.
Yan C J, Tian Z X, Fang Y W, Yang Y C, Li J, Zeng S Y, Gu S L, Xu C W, Tang S Z, Gu M H. 2011. Genetic analysis of starch paste viscosity parameters in glutinous rice (Oryza sativa L.). Theoretical and Applied Genetics, 122, 63–76.
Yang J, Hu C, Hu H, Yu R, Xia Z, Ye X, Zhu J. 2008. QTL Network: Mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics, 24, 721–723.
Yang Y C, Ni D H, Song F S, Li L, Lu X Z, Li Z F, Yang J B. 2012. Identification of QTL for rice starch RVA profile properties under different ecological sites. Acta Agronomica Sinica, 38, 264–274. (in Chinese)
Yu C H, Meng C T, Yong P W, Meng Y L, Fu J W, Kae K H, Yue I H, Yann R L. 2014. Genetic factors responsible for eating and cooking qualities of rice grains in a recombinant inbred population of an inter-subspeci?c cross. Molecular Breeding, 34, 655–673.
Zhang Q F, Zhang Y D, Zhu Z, Zhao L, Zhao Q Y, Xu L, Wang C L. 2007. Analysis of inheritance and QTLs of rice starch viscosity (RVA profile) characteristics. China Journal of Rice Science, 21, 591–598. (in Chinese)
Zhang Y S, Jang L, Liu X, Liu S J, Chen L M, Zhai H C, Wan J M. 2010. Analysis of QTLs for starch RVA profile properties in the superior rice cultivar Koshihikari. China Journal of Rice Science, 24, 137–144. (in Chinese)
Zhao X, Fitzgerald M. 2013. Climate change: Implications for the yield of edible rice. PLoS ONE, 8, e66218.