QTLs underlying natural variation of root growth angle among rice cultivars with the same functional allele of DEEPER ROOTING 1

Rice

Volumn 8, Issue 1, 2015, Pages

  Kitomi, Yuka ^a   Kanno, Noriko ^a   Kawai, Sawako ^a   Mizubayashi, Tatsumi ^a   Fukuoka, Shuichi ^a   Uga, Yusaku ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

Author keywords

DRO1; Natural variation; Quantitative trait locus; Root growth angle; Root system architecture

Indexed keywords

EID: 84925325918     PISSN: 19398425     EISSN: 19398433     Source Type: Journal    
DOI: 10.1186/s12284-015-0049-2     Document Type: Article

References (55)

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. Arai-Sanoh Y, Takai T, Yoshinaga S, Nakano H, Kojima M, Sakakibara H, et al. (2014) Deep rooting conferred by DEEPER ROOTING 1 enhances rice yield in paddy fields. Sci Rep 4:5563
3. Araki H, Morita S, Tatsumi J, Iijima M (2002) Physio-morphological analysis on axile root growth in upland rice. Plant Prod Sci 5:286–293
4. Broman KW, Sen S (2009) A guide to QTL mapping with R/qtl. Springer, New York
5. Broman KW, Wu H, Sen S (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890
6. Christopher J, Christopher M, Jennings R, Jones S, Fletcher S, Borrell A, et al. (2013) QTL for root angle and number in a population developed from bread wheats (Triticum aestivum) with contrasting adaptation to water-limited environments. Theor Appl Genet 126:1563–1574
7. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971
8. Courtois B, Ahmadi N, Khowaja F, Price AH, Rami JF, Frouin J, et al. (2009) Rice root genetic architecture: meta-analysis from a drought QTL database. Rice 2:115–128
9. Fang Z, Xia K, Yang X, Grotemeyer MS, Meier S, Rentsch D, et al. (2013) Altered expression of the PTR/NRT1 homologue OsPTR9 affects nitrogen utilization efficiency, growth and grain yield in rice. Plant Biotechnol J 11:446–458
10. Fujita D, Trijatmiko KR, Tagle AG, Sapasap MV, Koide Y, Sasaki K, et al. (2013) NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars. Proc Natl Acad Sci U S A 110:20431–20436
11. Giehl RFH, von Wirén N (2014) Root nutrient foraging. Plant Physiol 166:509–517
12. Gowda VRP, Henry A, Yamauchi A, Shashidhar HE, Serraj R (2011) Root biology and genetic improvement for drought avoidance in rice. Field Crops Res 122:1–13
13. Hamada A, Nitta M, Nasuda S, Kato K, Fujita M, Matsunaka H, et al. (2012) Novel QTLs for growth angle of seminal roots in wheat (Triticum aestivum L.). Plant Soil 354:395–405
14. Herder GD, Isterdael GV, Beeckman T, Smet ID (2010) The roots of a new green revolution. Trends Plant Sci 15:600–607
15. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800
16. Inukai Y, Sakamoto T, Ueguchi-Tanaka M, Shibata Y, Gomi K, Umemura I, et al. (2005) Crown Rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling. Plant Cell 17:1387–1396
17. Jain M, Kaur N, Garg R, Thakur JK, Tyagi AK, Khurana JP (2006a) Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa). Funct Integr Genomics 6:47–59
18. Jain M, Tyagi AK, Khurana JP (2006b) Genome-wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family in rice (Oryza sativa). Genomics 88:360–371
19. Kamoshita A, Wade LJ, Ali ML, Pathan MS, Zjang J, Sarkarung S, et al. (2002) Mapping QTL for root morphology of a rice population adapted to rainfed lowland conditions. Theor Appl Genet 104:880–893
20. Kitomi Y, Inahashi H, Takehisa H, Sato Y, Inukaia Y (2012) OsIAA13-mediated auxin signaling is involved in lateral root initiation in rice. Plant Sci 190:116–122
21. Kitomi Y, Ito H, Hobo T, Aya K, Kitano H, Inukai Y (2011) The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling. Plant J 67:472–484
22. Kitomi Y, Ogawa A, Kitano H, Inukai Y (2008) CRL4 regulates crown root formation through auxin transport in rice. Plant Root 2:19–28
23. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175
24. Liao H, Yan XL, Rubio G, Beebe SE, Blair MW, Lynch JP (2004) Genetic mapping of basal root gravitropism and phosphorus acquisition efficiency in common bean. Funct Plant Biol 31:959–970
25. Liu H, Wang S, Yu X, Yu J, He X, Zhang S, et al. (2005) ARL1, a LOB domain protein required for adventitious root formation in rice. Plant J 43:47–56
26. Liu S, Wang J, Wang L, Wang X, Xue Y, Wu P, et al. (2009) Adventitious root formation in rice requires OsGNOM1 and is mediated by the OsPINs family. Cell Res 19:1110–1119
27. Lobet G, Couvreur V, Meunier F, Javaux M, Draye X (2014) Plant water uptake in drying soils. Plant Physiol 164:1619–1627
28. Lynch JP (2013) Steep, cheap and deep: an ideotype to optimize water and N acquisition by maize root systems. Ann Bot 112:347–357
29. Mace ES, Singh V, van Oosterom EJ, Hammer GL, Hunt CH, Jordan DR (2012) QTL for nodal root angle in sorghum (Sorghum bicolor L. Moench) co-locate with QTL for traits associated with drought adaptation. Theor Appl Genet 124:97–109
30. MacMillan K, Emrich K, Piepho HP, Mullins CE, Price AH (2006) Assessing the importance of genotype x environmental interaction for root traits in rice using a mapping population II: conventional QTL analysis. Theor Appl Genet 113:953–964
31. Morita Y, Kyozuka J (2007) Characterization of OsPID, the rice ortholog of PINOID, and its possible involvement in the control of polar auxin transport. Plant Cell Physiol 48:540–549
32. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8:4321–4325
33. Norton GJ, Aitkenhead MJ, Khowaja FS, Whalley WR, Price AH (2008) A bioinformatic and transcriptomic approach to identifying positional candidate genes without fine mapping: an example using rice root-growth QTLs. Genomics 92:344–352
34. Norton GJ, Price AH (2009) Mapping of quantitative trait loci for seminal root morphology and gravitropic response in rice. Euphytica 166:229–237
35. 2 populations from maize ‘B73’ x teosinte ‘Zea luxurians’. Plant Root 1:57–65
36. Price AH, Steele KA, Moore BJ, Barraclough PB, Clark LJ (2000) A combined RFLP and AFLP linkage map of upland rice used to identify QTLs for root-penetration ability. Theor Appl Genet 100:49–56
37. Price AH, Steele KA, Moore BJ, Jones RGW (2002) Upland rice grown in soil filled chambers and exposed to contrasting water-deficit regimes. II. Mapping QTLs for root morphology and distribution. Field Crop Res 76:25–43
38. Ray JD, Yu L, McCouch SR, Champoux MC, Wang G, Nguyen HT (1996) Mapping quantitative trait loci associated with root penetration ability in rice. Theor Appl Genet 92:627–636
39. Rich SM, Watt M (2013) Soil conditions and cereal root system architecture: review and considerations for linking Darwin and Weaver. J Exp Bot 64:1193–1208
40. Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, et al. (2013) Rice Annotation Project Database (RAP-DB): An integrative and interactive database for rice genomics. Plant Cell Physiol 54:e6
41. Trachsel S, Kaeppler SM, Brown KM, Lynch JP (2013) Maize root growth angles become steeper under low N conditions. Field Crops Res 140:18–31
42. Uga Y (2012) Quantitative measurement of root growth angle by using the basket method. In: Hardy B (ed) Shashidhar HE, Henry A. Methodologies for root drought studies in rice. IRRI, Metro Manila, Philippines
43. 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
44. Uga Y, Kitomi Y, Ishikawa S, Yano M (in press) Genetic improvement for root growth angle to enhance crop production. Breed Sci
45. Uga Y, Kitomi Y, Yamamoto E, Kanno N, Kawai S, Mizubayashi T, et al. (2015) A QTL for root growth angle on rice chromosome 7 is involved in the genetic pathway of DEEPER ROOTING 1. Rice 8:8
46. Uga Y, Okuno K, Yano M (2011) Dro1, a major QTL involved in deep rooting of rice under upland field conditions. J Exp Bot 62:485–2494
47. Uga Y, Sugimoto K, Ogawa S, Rane J, Ishitani M, Hara N, et al. (2013a) Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nat Genet 45:1097–1102
48. Uga Y, Yamamoto E, Kanno N, Kawai S, Mizubayashi T, Fukuoka S (2013b) A major QTL controlling deep rooting on rice chromosome 4. Sci Rep 3:3040
49. Wang D, Pei K, Fu Y, Sun Z, Li S, Liu H, et al. (2007) Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa). Gene 394:13–24
50. Xu M, Zhu L, Shou H, Wu P (2005) A PIN1 family gene, OsPIN1, involved in auxin-dependent adventitious root emergence and tillering in rice. Plant Cell Physiol 46:1674–1681
51. Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, et al. (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767
52. Yamamoto E, Yonemaru J, Yamamoto T, Yano M (2012) OGRO: The Overview of functionally characterized Genes in Rice online database. Rice 5:26
53. Yan WH, Wang P, Chen HX, Zhou HJ, Li QP, Wang CR, et al. (2011) A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. Mol Plant 4:319–330
54. Yonemaru J, Ebana K, Yano M (2014a) HapRice, a SNP haplotype database and a web tool for rice. Plant Cell Physiol 55:e9
55. Yonemaru J, Mizobuchi R, Kato H, Yamamoto T, Yamamoto E, Matasubara K, et al. (2014b) Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars. BMC Genomics 15:346