Dissecting Genetic Basis of Deep Rooting in Dongxiang Wild Rice
Received date: 2021-08-02
Accepted date: 2021-11-10
Online published: 2022-03-10
Deep rooting is an important trait in rice drought resistance. Genetic resources of deep-rooting varieties are valuable in breeding of water-saving and drought-resistant rice. In the present study, 234 BC2F7 backcross introgression lines were derived from a cross of Dongye 80 (an accession of Dongxiang wild rice as the donor parent) and R974 (an indica restorer line as the recurrent parent). A genetic linkage map containing 1 977 bin markers was constructed by ddRADSeq for QTL analysis. Thirty-one QTLs for four root traits (the number of deep roots, the number of shallow roots, the total number of deep roots and the ratio of deep roots) were assessed on six rice chromosomes in two environments (2020 Shanghai and 2021 Hainan). Two of the QTLs, qDR5.1 and qTR5.2, were located on chromosome 5 in a 70-kb interval. They were detected in both environments. qDR5.1 explained 13.35% of the phenotypic variance in 2020 Shanghai and 12.01% of the phenotypic variance in 2021 Hainan. qTR5.2 accounted for 10.88% and 10.93% of the phenotypic variance, respectively. One QTL (qRDR2.2) for the ratio of deep roots was detected on chromosome 2 in a 210-kb interval and accounted for 6.72% of the phenotypic variance in 2020. The positive effects of these three QTLs were all from Dongxiang wild rice. Furthermore, nine and four putative candidate genes were identified in qRDR2.2 and qDR5.1/qTR5.2, respectively. These findings added to our knowledge of the genetic control of root traits in rice. In addition, this study will facilitate the future isolation of candidate genes of the deep-rooting trait and the utilization of Dongxiang wild rice in the improvement of rice drought resistance.
Nie Yuanyuan, Xia Hui, Ma Xiaosong, Lou Qiaojun, Liu Yi, Zhang Anling, Cheng Liang, Yan Longan, Luo Lijun . Dissecting Genetic Basis of Deep Rooting in Dongxiang Wild Rice[J]. Rice Science, 2022 , 29(3) : 277 -287 . DOI: 10.1016/j.rsci.2021.11.002
| [1] | Abe J, Morita S. 1994. Growth direction of nodal roots in rice: Its variation and contribution to root system formation. Plant Soil, 165: 333-337. |
| [2] | Aloni R, Aloni E, Langhans M, Ullrich C I. 2006. Role of cytokinin and auxin in shaping root architecture: Regulating vascular differentiation, lateral root initiation, root apical dominance and root gravitropism. Ann Bot, 97: 883-893. |
| [3] | Araki H, Morita S, Tatsumi J, Iijima M. 2002. Physiol-morphological analysis on axile root growth in upland rice. Plant Prod Sci, 5: 286-293. |
| [4] | Blum A. 2005. Drought resistance, water-use efficiency, and yield potential: Are they compatible, dissonant, or mutually exclusive? Aust J Agric Res, 56: 1159-1168. |
| [5] | Bradbury-Jones C, Sambrook S, Irvine F. 2007. The meaning of empowerment for nursing students: A critical incident study. J Adv Nurs, 59(4): 342-351. |
| [6] | Campo S, Baldrich P, Messeguer J, Lalanne E, Coca M, San Segundo B. 2014. Overexpression of a calcium-dependent protein kinase confers salt and drought tolerance in rice by preventing membrane lipid peroxidation. Plant Physiol, 165(2): 688-704. |
| [7] | Fukai S, Cooper M. 1995. Development of drought-resistant cultivars using physiomorphological traits in rice. Field Crops Res, 40: 67-86. |
| [8] | Gowda V R P, Henry A, Yamauchi A, Shashidhar H E, Serraj R. 2011. Root biology and genetic improvement for drought avoidance in rice. Field Crops Res, 122: 1-13. |
| [9] | Kato Y, Abe J, Kamoshita A, Yamagishi J. 2006. Genotypic variation in root growth angle in rice (Oryza sativa L.) and its association with deep root development in upland fields with different water regimes. Plant Soil, 287: 117-129. |
| [10] | Kitomi Y, Kanno N, Kawai S, Mizubayashi T, Fukuoka S, Uga Y. 2015. QTLs underlying natural variation of root growth angle among rice cultivars with the same functional allele of DEEPER ROOTING 1. Rice, 8: 16. |
| [11] | Kondo M, Murty M V R, Aragones D V. 2000. Characteristics of root growth and water uptake from soil in upland rice and maize under water stress. Soil Sci Plant Nutr, 46: 721-732. |
| [12] | Kondo M, Pablico P P, Aragones D V, Agbisit R, Abe J, Morita S, Courtois B. 2003. Genotypic and environmental variations in root morphology in rice genotypes under upland field conditions. Plant Soil, 255: 189-200. |
| [13] | Liang Y S, Zheng J, Yan C, Li X X, Liu S F, Zhou J J, Qin X J, Nan W B, Yang Y Q, Zhang H M. 2018. Locating QTLs controlling overwintering trait in Chinese perennial Dongxiang wild rice. Mol Genet Genomics, 293(1): 81-93. |
| [14] | Löfke C, Zwiewka M, Heilmann I, van Montagu M C E, Thomas Teichmann T, Friml J. 2013. Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. Proc Natl Acad Sci USA, 110(9): 3627-3632. |
| [15] | Lou Q J, Chen L, Mei H W, Wei H B, Feng F J, Wang P, Xia H, Li T M, Luo L J. 2015. Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice. J Exp Bot, 66: 4749-4757. |
| [16] | Luo L J. 2010. Breeding for water-saving and drought-resistance rice (WDR) in China. J Exp Bot, 61: 3509-3517. |
| [17] | Luo L J, Zhang Q F. 2001. The status and strategy on drought resistance of rice (Oryza sativa L.). Chin J Rice Sci, 15(3): 209-214. (in Chinese with English abstract) |
| [18] | McCouch S R, CGSNL(Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative). 2008. Gene nomenclature system for rice. Rice, 1(1): 72-84. |
| [19] | Pandit E, Panda R K, Sahoo A, Pani D R, Pradhan S K. 2020. Genetic relationship and structure analysis of root growth angle for improvement of drought avoidance in early and mid-early maturing rice genotypes. Rice Sci, 27(2): 124-132. |
| [20] | Price A H, Cairns J E, Horton P, Jones H G, Griffiths H. 2002. Linking drought-resistance mechanisms to drought avoidance in upland rice using a QTL approach: Progress and new opportunities to integrate stomatal and mesophyll responses. J Exp Bot, 53: 989-1004. |
| [21] | Qi W D, Chen H P, Yang Z Z, Hu B L, Luo X D, Ai B, Luo Y, Huang Y, Xie J K, Zhang F T. 2020. Systematic characterization of long non-coding RNAs and their responses to drought stress in Dongxiang wild rice. Rice Sci, 27(1): 21-31. |
| [22] | Singh M, Gupta A, Laxmi A. 2014. Glucose and phytohormone interplay in controlling root directional growth in Arabidopsis. Plant Signal Behav, 9: e29219. |
| [23] | Turner N C. 1996. Further progress in crop water relations. Adv Agron, 58(8): 293-338. |
| [24] | Uga Y. 2012. Quantitative measurement of root growth angle by using the basket method. In: Shashidhar H E, Henry A, Hardy B. Methodologies for Root Drought Studies in Rice. Manila, the Philippines: International Rice Research Institute: 22-26. |
| [25] | Uga Y, Okuno K, Yano M. 2011. Dro1, a major QTL involved in deep rooting of rice under upland field conditions. J Exp Bot, 62: 2485-2494. |
| [26] | Uga Y, Hanzawa E, Nagai S, Sasaki K, Yano M, Sato T. 2012. Identification of qSOR1, a major rice QTL involved in soil- surface rooting in paddy fields. Theor Appl Genet, 124: 75-86. |
| [27] | Uga Y, Yamamoto E, Kanno N, Kawai S, Mizubayashi T, Fukuoka S. 2013a. A major QTL controlling deep rooting on rice chromosome 4. Sci Rep, 3: 3040. |
| [28] | Uga Y, Sugimoto K, Ogawa S, Rane J, Ishitani M, Hara N, Kitomi Y, Inukai Y, Ono K, Kanno N, Inoue H, Takehisa H, Motoyama R, Nagamura Y, Wu J Z, Matsumoto T, Takai T, Okuno K, Yano M. 2013b. Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nat Genet, 45: 1097-1102. |
| [29] | Uga Y, Kitomi Y, Yamamoto E, Kanno N, Kawai S, Mizubayashi T, Fukuoka S. 2015. A QTL for root growth angle on rice chromosome 7 is involved in the genetic pathway of DEEPER ROOTING 1. Rice, 8: 8. |
| [30] | Xia H, Luo Z, Xiong J, Ma X S, Lou Q J, Wei H B, Qiu J, Yang H, Liu G L, Fan L J, Chen L, Luo L J. 2019. Bi-directional selection in upland rice leads to its adaptive differentiation from lowland rice in drought resistance and productivity. Mol Plant, 12: 170-184. |
| [31] | Xie W B, Feng Q, Yu H H, Huang H H, Zhao Q, Xing Y Z, Yu S B, Han B, Zhang Q F. 2010. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci USA, 107(23): 10578-10583. |
| [32] | Yoshida S, Hasegawa S. 1982. The rice root system: Its development and function. In: The Rice Root System: Its Development and Function in Drought Resistance in Crops with Emphasis on Rice. Manila, the Philippines: International Rice Research Institute: 97-114. |
| [33] | Yuan J, Chen D, Ren Y J, Zhang X L, Zhao J. 2008. Characteristic and expression analysis of a metallothionein gene, OsMT2b, down-regulated by cytokinin suggests functions in root development and seed embryo germination of rice. Plant Physiol, 146(4): 1637-1650. |
| [34] | Zhang F T, Luo X D, Zhou Y, Xie J K. 2016. Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.). Biotechnol Lett, 38(4): 711-721. |
| [35] | Zhang Q F. 2007. Strategies for developing green super rice. Proc Natl Acad Sci USA, 104: 16402-16409. |
| [36] | Zhang X, Zhou S X, Fu Y C, Su Z, Wang X K, Sun C Q. 2006. Identification of a drought tolerant introgression line derived from Dongxiang common wild rice (O. rufipogon Griff.). Plant Mol Biol, 62: 247-259. |
/
| 〈 |
|
〉 |