Advertisement

Planta

, Volume 250, Issue 1, pp 129–143 | Cite as

A novel QTL QTrl.saw-2D.2 associated with the total root length identified by linkage and association analyses in wheat (Triticum aestivum L.)

  • Xingwei Zheng
  • Xiaojie Wen
  • Ling Qiao
  • Jiajia Zhao
  • Xiaojun Zhang
  • Xin Li
  • Shuwei Zhang
  • Zujun Yang
  • Zhijian Chang
  • Jianli ChenEmail author
  • Jun ZhengEmail author
Original Article

Abstract

Main conclusion

In wheat, a QTL QTrl.saw-2D.2 associated with the total root length was identified, presumably containing genes closely related to root development.

A mapping population of 184 recombinant inbred lines derived from the cross SY95-71 × CH7034 was used to map QTL for seedling root characteristics in hydroponic culture (HC) and in soil-filled pot (SP) methods. Four traits, including maximum root length (MRL), root number (RN), total length (TRL), and root diameter (RD) were measured and used in QTL analyses. A total of 33 QTL for the four root traits were detected, 17 QTLs for TRL, six for RN, seven for MRL, and three for RD. Seven QTL were detected in both HC and SP methods, which explained 7–18% phenotypic variation. One QTL QTrl.saw-2D.2 detected in both HC and SP methods was also validated in another population comprised of 215 diverse lines. This QTL is a novel QTL that explained the highest phenotypic variation 18% in all QTL identified in the present study. Based on candidate gene and comparative genomics analyses, the QTL QTrl.saw-2D.2 may contain genes closely related to root development in wheat (Triticum aestivum L.). The two candidate genes were proposed to explore in future studies.

Keywords

Drought tolerance coefficient Quantitative trait locus Stay green Total root length Yield components 

Abbreviations

DL

Dryland conditions

DTC

Drought tolerance coefficient

HC

Hydroponic culture

KNS

Kernel number per spike

MRL

Maximum root length

RD

Root diameter

RIL

Recombinant inbred line

RN

Root number

SL

Spike length

SN

Spikelet number per spike

SP

Pots containing soil

TKW

Thousand kernel weight

TRL

Total root length

WW

Well-watered condition

Notes

Acknowledgements

This work was funded by National Key Research and Development Program of China (2017YFD0100600), Agricultural Science and Technology Project (YCX2018413, 17yzgc010), Natural Science Foundation of Shanxi Province (2016011001, 201703D211007). We thank Dr. Robert A McIntosh (University of Sydney) for help with manuscript improvement.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

425_2019_3154_MOESM1_ESM.tif (1.6 mb)
Supplementary material 1 (TIFF 1637 kb)
425_2019_3154_MOESM2_ESM.xlsx (160 kb)
Supplementary material 2 (XLSX 160 kb)
425_2019_3154_MOESM3_ESM.xlsx (13 kb)
Supplementary material 3 (XLSX 13 kb)
425_2019_3154_MOESM4_ESM.xlsx (18 kb)
Supplementary material 4 (XLSX 17 kb)
425_2019_3154_MOESM5_ESM.xlsx (14 kb)
Supplementary material 5 (XLSX 13 kb)
425_2019_3154_MOESM6_ESM.xlsx (16 kb)
Supplementary material 6 (XLSX 15 kb)

References

  1. Atkinson JA, Wingen LU, Griffiths M, Pound MP, Gaju O, Foulkes MJ, Gouis JL, Griffiths S, Bennett MJ, King J et al (2015) Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat. J Exp Bot 66:2283–2292CrossRefPubMedPubMedCentralGoogle Scholar
  2. Ayalew H, Liu H, Yan G (2017) Identification and validation of root length QTLs for water stress resistance in hexaploid wheat (Titicum aestivum L.). Euphytica 213:126.  https://doi.org/10.1007/s10681-017-1914-4 CrossRefGoogle Scholar
  3. Azevedo MCB, Chopart JL, Sugarcane CCM (2011) Root length density and distribution from root intersection counting on a trench-profile. Sci Agricola 68:94–101CrossRefGoogle Scholar
  4. Bai CH, Liang YL, Hawkesford MJ (2013) Identifcation of QTLs associated with seedling root traits and their correlation with plant height in wheat. J Exp Bot 64:1745–1753CrossRefPubMedPubMedCentralGoogle Scholar
  5. Börner A, Schumann E, Fürste A, Coster H, Leithold B, Roder MS, Weber WE (2002) Mapping of quantitative trait locus determining agronomic important characters in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet 105:921–936CrossRefPubMedGoogle Scholar
  6. Box JE, Ramsuer EL (1993) Minirhizotron wheat root data: comparisons to soil core root data. Agron J 85:1058–1060CrossRefGoogle Scholar
  7. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635CrossRefPubMedGoogle Scholar
  8. Canè MA, Maccaferri M, Nazemi G, Salvi S, Francia R, Colalongo C, Tuberosa R (2014) Association mapping for root architectural traits in durumwheat seedlings as related to agronomic performance. Mol Breeding 34:1629–1645CrossRefGoogle Scholar
  9. Cao P, Ren YZ, Zhang KP, Teng W, Zhao XQ, Dong ZY, Liu X, Qin HJ, Li ZS, Wang DW et al (2014) Further genetic analysis of a major quantitative trait locus controlling root length and related traits in common wheat. Mol Breed 33:975–985CrossRefGoogle Scholar
  10. Casson SA, Topping JF, Lindsey K (2009) MERISTEM-DEFECTIVE, an RS domain protein, is required for the correct meristem patterning and function in Arabidopsis. Plant J 57:857–869CrossRefPubMedGoogle Scholar
  11. Chen RF, Ji FM, Guan JW, Deng JM (2015) Advanced and prospects in plant symmetric and asymmetric competition. Chinese J Plant Ecol 39:530–540 (in Chinese with English abstract) CrossRefGoogle Scholar
  12. Chen DD, Richardson T, Chai SC, Lynne Mcintyre C, Rae AL, Xue GP (2016) Drought-up-regulated TaNAC69-1 is a transcriptional repressor of TaSHY2 and TaIAA7, and enhances root length and biomass in wheat. Plant Cell Physiol 57:2076–2090CrossRefPubMedGoogle Scholar
  13. Chen DD, Chai SC, Lynne Mcintyre C, Xue GP (2018) Overexpression of a predominantly root-expressed NAC transcription factor in wheat roots enhances root length, biomass and drought tolerance. Plant Cell Rep 37:225–237CrossRefGoogle Scholar
  14. Cho SK, Ryu MY, Song C, Kwak JM, Kim WT (2008) Arabidopsis PUB22 and PUB23 are homologous U-box E3 ubiquitin ligases that play combinatory roles in response to drought stress. Plant Cell 20:1899–1914CrossRefPubMedPubMedCentralGoogle Scholar
  15. Cui F, Zhang N, Fan XL, Zhang W, Zhao HC, Yang LJ, Pan RQ, Chen M, Han J, Zhao XQ et al (2017) Utilization of a wheat 660 K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number. Sci Rep 7:3788CrossRefPubMedPubMedCentralGoogle Scholar
  16. Cuthbert JL, Somers DJ, Brule-Babel AL, Brown PD, Crow GH (2008) Molecular mapping of quantitative trait loci for yield and yield components in spring wheat (Triticum aestivum L.). Theor Appl Genet 117:595–608CrossRefPubMedGoogle Scholar
  17. Francki MG, Walker E, Crawford AC, Broughton S, Ohm HW, Barclay I, Wilson RE, McLean R (2009) Comparison of genetic and cytogenetic maps of hexaploid wheat (Triticum aestivum L.) using SSR and DArT markers. Mol Genet Genom 281:181–191CrossRefGoogle Scholar
  18. Frova C, Krajewski P, Fonzo ND, Villa M, Sari-Gorla M (1999) Genetic analysis of drought tolerance in maize by molecular markers I. Yield components. Theor Appl Genet 99:280–288CrossRefGoogle Scholar
  19. Guan PF, Lu LH, Jia JL, Kabir MR, Zhang JB, Lan TY, Zhao Y, Xin MM, Hu ZR, Yao YY et al (2018) Global QTL analysis identifies genomic regions on chromosomes 4A and 4B harboring stable loci for yield-related traits across different environments in wheat (Triticum aestivum L.). Front Plant Sci 9:529CrossRefPubMedPubMedCentralGoogle Scholar
  20. Guo J, Shi WP, Zhang Z, Cheng JY, Sun DZ, Yu J, Li XL, Guo PY, Hao CY (2018) Association of yield-related traits in founder genotypes and derivatives of common wheat (Triticum aestivum L.). BMC Plant Biol 18:38CrossRefPubMedPubMedCentralGoogle Scholar
  21. He X, Qu BY, Li WJ, Zhao XQ, Teng W, Ma WY, Ren Y, Li B, Li ZS, Tong YP (2015) The nitrate-inducible NAC transcription factor TaNAC2-5A controls nitrate response and increases wheat yield. Plant Physiol 169:1991–2005PubMedPubMedCentralGoogle Scholar
  22. Howell T, Hale I, Jankuloski L, Bonafede M, Gilbert M, Dubcovsky J (2014) Mapping a region within the 1RS.1BL translocation in common wheat affecting grain yield and canopy water status. Theor Appl Genet 127:2695–2709CrossRefPubMedPubMedCentralGoogle Scholar
  23. Hu ZR, Wang R, Zheng M, Liu XB, Meng F, Wu HL, Yao YY, Xin MM, Peng HR, Ni ZF et al (2018) TaWRKY51 promotes lateral root formation through negatively regulating ethylene biosynthesis in wheat (Triticum aestivum L.). Plant J 96:372–388CrossRefPubMedGoogle Scholar
  24. Jia HY, Wan HS, Yang SH, Zhang ZZ, Kong ZX, Xue SL, Zhang LX, Ma ZQ (2013) Genetic dissection of yield-related traits in a recombinant inbred line population created using a key breeding parent in China’s wheat breeding. Theor Appl Genet 126:2123–2139CrossRefPubMedGoogle Scholar
  25. Jose S, Gillespie AR, Seifert JR, Pope PE (2001) Comparison of minirhizotron and soil core methods for quantifying root biomass in a temperate alley cropping system. Agrofor Syst 2:161–168CrossRefGoogle Scholar
  26. Joshi A, Kumar S, Rane J (2007) Stay green trait: variation, inheritance and its association with spot blotch resistance in spring wheat (Triticum aestivum L.). Euphytica 153:59–71CrossRefGoogle Scholar
  27. Kabir MR, Liu G, Guan PF, Wang F, Khan AA, Ni ZF, Yao YY, Hu ZR, Xin MM, Peng HR et al (2015) Mapping QTLs associated with root traits using two different populations in wheat (Triticum aestivum L.). Euphytica 206:175–190CrossRefGoogle Scholar
  28. Kumar N, Kulwal PL, Balyan HS, Gupta PK (2007) QTL mapping for yield and yield contributing traits in two mapping populations of bread wheat. Mol Breed 19:163–177CrossRefGoogle Scholar
  29. Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199PubMedPubMedCentralGoogle Scholar
  30. Lei L, Li G, Zhang H, Powers CA, Fang TL, Chen YH, Wang SW, Zhu XK, Carver BF, Yan LL (2017) Nitrogen use efficiency is regulated by interacting proteins relevant to development in wheat. Plant Biotechnol J 16:1214–1226CrossRefGoogle Scholar
  31. Li ZK, Peng T, Zhang WD, Xie QG, Tian JC (2010) Analysis of QTLs for root traits at seedling stage using an “Immortalized F 2″ population of wheat. Acta Agronomica Sinica 36:1764–1778 (in Chinese with English abstract) Google Scholar
  32. Li P, Chen J, Wu P, Zhang J, Chu C, See D, Brown-Guedira G, Zemetra R, Souza E (2011) Quantitative trait loci analysis for the effect of Rht-B1 dwarfing gene on coleoptile length and seedling root length and number of bread wheat. Crop Sci 51:2561–2568CrossRefGoogle Scholar
  33. Li B, Liu D, Li QR, Mao XG, Li A, Wang JY, Chang XP, Jing RL (2016) Overexpression of wheat gene TaMOR improves root system architecture and grain yield in Oryza sativa. J Exp Bot 67:4155–4167CrossRefPubMedPubMedCentralGoogle Scholar
  34. Liu XL, Chang XP, Li RZ, Jing RL (2011) Mapping QTLs for seminal root architecture and coleoptile length in wheat. Acta Agronomica Sinica 37:381–388 (in Chinese with English abstract) CrossRefGoogle Scholar
  35. Liu XL, Li RZ, Chang XP, Jing RL (2013) Mapping QTLs for seedling root traits in a doubled haploid wheat population under different water regimes. Euphytica 189:51–66CrossRefGoogle Scholar
  36. Luo PG, Zhang HY, Shu K, Wu XH, Zhang HQ, Ren ZL (2009) The physiological genetic effects of 1BL/1RS translocated chromosome in ‘stay green’ wheat cultivars CN17. Can J Plant Sci 89:1–10CrossRefGoogle Scholar
  37. Ma ZQ, Zhao DM, Zhang CQ, Zhang ZZ, Xue SL, Lin F, Kong ZX, Tian DG, Luo QY (2007) Molecular genetic analysis of five spike related traits in wheat using RIL and immortalized F2 populations. Mol Genet Genom 277:31–42CrossRefGoogle Scholar
  38. Ma J, Luo W, Zhang H, Zhou XH, Qin NN, Wei YM, Liu YX, Jiang QT, Chen GY, Zheng YL et al (2017) Identification of quantitative trait loci for seedling root traits from Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum). Genome 60:1068–1075CrossRefPubMedGoogle Scholar
  39. Maccaferri M, El-Feki W, Nazemi G, Salvi S, Cane MA, Colalongo MC, Stefanelli S, Tuberosa R (2016) Prioritizing quantitative trait loci for root system architecture in tetraploid wheat. J Exp Bot 67:1161–1178CrossRefPubMedPubMedCentralGoogle Scholar
  40. Marza F, Bai GH, Carver BF, Zhou WC (2006) Quantitative trait loci for yield and related traits in the wheat population Ning7840/Clark. Theor Appl Genet 112:688–698CrossRefPubMedGoogle Scholar
  41. Meng L, Li HH, Zhang LY, Wang JK (2015) QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J 3:269–283CrossRefGoogle Scholar
  42. Ni ZF, Li HJ, Zhao Y, Peng HR, Hu ZR, Xin MM, Sun QX (2018) Genetic improvement of heat tolerance in wheat: recent progress in understanding the underlying molecular mechanisms. Crop J 6:32–41CrossRefGoogle Scholar
  43. Petricka JJ, Clay NK, Nelson TM (2008) Vein patterning screens and the defectively organized tributaries mutants in Arabidopsis thaliana. Plant J 56:251–263CrossRefPubMedGoogle Scholar
  44. Qi W, Tang Y, Zhu W, Li DY, Diao CD, Xu LL, Zeng J, Wang Y, Fan X, Sha L et al (2016) Molecular cytogenetic characterization of a new wheat-rye 1BL•1RS translocation line expressing superior stripe rust resistance and enhanced grain yield. Planta 244:405–416CrossRefPubMedGoogle Scholar
  45. Ren Y, He X, Liu D, Li J, Zhao X, Li B, Tong Y, Zhang A, Li Z (2012) Major quantitative trait loci for seminal root morphology of wheat seedlings. Mol Breed 30:139–148CrossRefGoogle Scholar
  46. Ren YZ, Qian YY, Xu YH, Zou CQ, Liu DC, Zhao XQ, Zhang AM, Tong YP (2017) Characterization of QTLs for root traits of wheat grown under different nitrogen and phosphorus supply levels. Front Plant Sci 8:2096CrossRefPubMedPubMedCentralGoogle Scholar
  47. SAS Institute Inc (1999) SAS OnlineDoc®, version 8. SAS Institute Inc, Cary, NCGoogle Scholar
  48. Sharp RE, Poroyko V, Hejlek LG, Spollen WG, Springer GK, Bohnert HJ, Nguyen HT (2004) Root growth maintenance during water deficits: physiology to functional genomics. J Exp Bot 55:2343–2351CrossRefGoogle Scholar
  49. Shewry PR (2009) Wheat. J Exp Bot 60:1537–1553CrossRefPubMedGoogle Scholar
  50. Shi WP, Hao CY, Zhang Y, Chen JY, Zhang Z, Liu J, Yi X, Xu YH, Zhang XY, Cheng SH et al (2017) A combined association mapping and linkage analysis of kernel number per spike in common wheat (Triticum aestivum L.). Front Plant Sci 8:1412CrossRefPubMedPubMedCentralGoogle Scholar
  51. Soriano JM, Royo C (2015) Dissecting the genetic architecture of leaf rust resistance in wheat by QTL meta-analysis. Phytopathology 105:1585–1593CrossRefPubMedGoogle Scholar
  52. Steinemann S, Zeng ZH, McKay A, Heuer S, Langridge P, Huang CY (2015) Dynamic root responses to drought and rewatering in two wheat (Triticum aestivum) genotypes. Plant Soil 391:139–152CrossRefGoogle Scholar
  53. Uga Y, Kitomi Y, Ishikawa S, Yano M (2015) Genetic improvement for root growth angle to enhance crop production. Breed Sci 65:111–119CrossRefPubMedPubMedCentralGoogle Scholar
  54. Vamerali T, Bandiera M, Mosca G (2012) Minirhizotrons in modern root studies. In: Mancuso S (ed) Measuring roots. Springer, Berlin, Heidelberg, pp 341–361CrossRefGoogle Scholar
  55. Van Ooijen JW (2006) JoinMap® 4.0: software for the calculation of genetic linkage maps in experimental population. Kyazma BV, Wageningen, The NetherlandsGoogle Scholar
  56. Vepraskas MJ, Hoyt GD (1988) Comparison of the trench-profile and core methods for evaluating root distributions in tillage studies. Agron J 80:166–172CrossRefGoogle Scholar
  57. Voss-Fels KP, Robinson H, Mudge SR, Richard C, Newman S, Wittkop B, Stahl A, Friedt W et al (2018) VERNALIZATION1 modulates root system architecture in wheat and barley. Mol Plant 11:226–229CrossRefPubMedGoogle Scholar
  58. Wang FH, Wang XQ, Li SJ, Bian ML, Yu ZW, Yu SL (2001) Studies on the root activities in different layers of soil of high-yielding wheat at the late growth period. Acta Agron Sinica 27:891–895 (In Chinese with English abstract) Google Scholar
  59. Wang RX, Hai L, Zhang XY, You GX, Yan CS, Xiao SH (2009) QTL mapping for grain filling rate and yield-related traits in RILs of the Chinese winter wheat population Heshangmai × Yu8679. Theor Appl Genet 118:313–325CrossRefPubMedGoogle Scholar
  60. Wang SC, Basten CJ, Zeng ZB (2012) Windows QTL cartographer 2.5. Department of statistics, North Carolina State University, Raleigh, NC, USA. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm. Accessed 1 Aug 2012
  61. Wang J, Xiong Y, Li F, Siddique KHM, Turner NC (2017) Effects of drought stress on morphophysiological traits, biochemical characteristics, yield, and yield components in different ploidy wheat: a meta-analysis. Adv Agron 143:139–173CrossRefGoogle Scholar
  62. Wang HF, Hu ZR, Huang K et al (2018) Three genomes differentially contribute to the seedling lateral root number in allohexaploid wheat: evidence from phenotype evolution and gene expression. Plant J 95:976–987CrossRefPubMedGoogle Scholar
  63. Wasson AP, Richards RA, Chatrath R, Misra SC, Sai Prasad SV, Rebetzke GJ, Kirkegaard JA, Christopher J, Watt M (2012) Traits and selection strategies to improve root systems and water uptake in water-limited wheat crops. J Exp Bot 63: 3485–3498CrossRefPubMedGoogle Scholar
  64. Wasson AP, Richards RA, Chatrath R, Misra SC, Prasad SVS, Rebetzke GJ, Kirkegaard JA, Winfield MO, Allen AM, Burridge AJ et al (2016) High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool. Plant Biotechnol J 14:1195–1206CrossRefGoogle Scholar
  65. Xie Q, Fernando KMC, Mayes S, Sparkes DL (2017) Identifying seedling root architectural traits associated with yield and yield components in wheat. Ann Bot 119:1115–1129CrossRefPubMedPubMedCentralGoogle Scholar
  66. Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X et al (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767CrossRefPubMedGoogle Scholar
  67. Zhai HJ, Feng ZY, Li J, Liu XY, Xiao SH, Ni ZF, Sun QX (2016) QTL analysis of spike morphological traits and plant height in winter wheat (Triticum aestivum L.) using a high-density SNP and SSR-based linkage map. Front Plant Sci 7:1617PubMedPubMedCentralGoogle Scholar
  68. Zhang ZB, Xu P (2002) Reviewed on wheat genome. Hereditas 24:389–394 (In Chinese with English abstract) PubMedGoogle Scholar
  69. Zhang LY, Liu DC, Guo XL, Yang WL, Sun JZ, Wang DW, Zhang AM (2010a) Genomic distribution of quantitative trait loci for yield and yield-related traits in common wheat. J Integr Plant Biol 52:996–1007CrossRefPubMedGoogle Scholar
  70. Zhang ZW, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu JM, Arnett DK, Ordovas JM et al (2010b) Mixed linear model approach adapted for genome-wide association studies. Nat Genetics 42:355–360CrossRefPubMedGoogle Scholar
  71. Zhang JN, Hao CY, Ren Q, Chang XP, Liu GR, Jing RL (2011) Association mapping of dynamic developmental plant height in common wheat. Planta 234:891–902CrossRefPubMedGoogle Scholar
  72. Zhou SH, Wu QH, Xie JZ, Chen JJ, Chen YX, Fu L, Wang GX, Yu MH, Wang ZZ, Zhang DY et al (2016) Mapping QTLs for wheat seedling traits in RILs population of Yanda 1817 × Beinong 6 under normal and salt-stress conditions. Acta Agronomica Sinica 42:1764–1778 (In Chinese with English abstract) CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Xingwei Zheng
    • 1
  • Xiaojie Wen
    • 2
  • Ling Qiao
    • 1
  • Jiajia Zhao
    • 1
  • Xiaojun Zhang
    • 3
  • Xin Li
    • 3
  • Shuwei Zhang
    • 3
  • Zujun Yang
    • 3
  • Zhijian Chang
    • 3
  • Jianli Chen
    • 4
    Email author
  • Jun Zheng
    • 1
    Email author
  1. 1.Institute of Wheat ResearchShanxi Academy of Agricultural SciencesLinfenChina
  2. 2.Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
  3. 3.The Shanxi Province Key Laboratory of Crop Genetics and Gene Improvement, Institute of Crop ScienceShanxi Academy of Agricultural SciencesTaiyuanChina
  4. 4.Department of Plant SciencesUniversity of IdahoAberdeenUSA

Personalised recommendations