Planta

, Volume 243, Issue 2, pp 459–471 | Cite as

A comprehensive meta-analysis of plant morphology, yield, stay-green, and virus disease resistance QTL in maize (Zea mays L.)

  • Yijun Wang
  • Jing Xu
  • Dexiang Deng
  • Haidong Ding
  • Yunlong Bian
  • Zhitong Yin
  • Yarong Wu
  • Bo Zhou
  • Ye Zhao
Original Article

Abstract

Main conclusion

The meta-QTL and candidate genes will facilitate the elucidation of molecular bases underlying agriculturally important traits and open new avenues for functional markers development and elite alleles introgression in maize breeding program.

A large number of QTLs attributed to grain productivity and other agriculturally important traits have been identified and deposited in public repositories. The integration of fruitful QTL becomes a major issue in current plant genomics. To this end, we first collected QTL for six agriculturally important traits in maize, including yield, plant height, ear height, leaf angle, stay-green, and maize rough dwarf disease resistance. The meta-analysis method was then employed to retrieve 113 meta-QTL. Additionally, we also isolated candidate genes for target traits by the bioinformatic technique. Several candidates, including some well-characterized genes, GA3ox2 for plant height, lg1 and lg4 for leaf angle, zfl1 and zfl2 for flowering time, were co-localized with established meta-QTL intervals. Intriguingly, in a relatively narrow meta-QTL region, the maize ortholog of rice yield-related gene GW8/OsSPL16 was believed to be a candidate for yield. Leveraging results presented in this study will provide further insights into the genetic architecture of maize agronomic traits. Moreover, the meta-QTL and candidate genes reported here could be harnessed for the enhancement of stress tolerance and yield performance in maize and translation to other crops.

Keywords

Agronomic trait Bioinformatics Candidate gene Maize breeding Meta-analysis Quantitative trait locus Yield performance 

Abbreviations

BR

Brassinosteroid

GA

Gibberellin

GWAS

Genome-wide association studies

QTL

Quantitative trait locus

SBP

SQUAMOSA promoter binding protein

Supplementary material

425_2015_2419_MOESM1_ESM.tif (18 kb)
QTL distribution in the maize genome. QTL for yield, plant height, and ear height are located in all ten chromosomes. QTL for leaf angle are in all ten chromosomes except chromosomes 6, 7, and 10. QTL for stay-green are positioned in chromosomes 4, 7, and 10. QTL for maize rough dwarf disease resistance are distributed in chromosomes 2, 6, 7, 8, and 10 (TIFF 18 kb)
425_2015_2419_MOESM2_ESM.pptx (397 kb)
Consensus map of collected maize QTL (PPTX 397 kb)
425_2015_2419_MOESM3_ESM.tif (97 kb)
Characterization of meta-QTL MQTL26 for maize yield. Four meta-QTL (from MQTL24 to MQTL27) are identified by the meta-analysis of eighteen QTL, including fourteen QTL for yield, two QTL for plant height, one QTL for ear height and leaf angle each. The meta-QTL MQTL26 is within a relatively narrow interval with estimated size of 346 kb. The maize ortholog of rice yield-related genes GW8/OsSPL16 in MQTL26 region is believed to be a candidate for yield. Four meta-QTL regions are delimited in color (TIFF 97 kb)
425_2015_2419_MOESM4_ESM.tif (92 kb)
Characterization of meta-QTL MQTL77 for maize yield. Two meta-QTL (MQTL76 and MQTL77) are identified by the meta-analysis of twenty-four yield-related QTL, including nine QTL for kernel weight, six QTL for ear length, three QTL for kernel number per row and kernel ratio each, and one QTL for ear diameter, ear weight, and kernel row number each. Of note, eighteen QTL collected from independent analysis display similar confidence intervals and varied peaks. The MQTL77 is at a nearly 12 cM interval containing sixty-five putative transcripts. The maize ortholog of rice yield-related genes DEP1 in MQTL77 region is believed to be a candidate for yield. Two meta-QTL regions are delimited in color (TIFF 92 kb)
425_2015_2419_MOESM5_ESM.xlsx (118 kb)
Putative transcripts in meta-QTL regions (XLSX 117 kb)
425_2015_2419_MOESM6_ESM.doc (106 kb)
Other leaf architecture-related genes (DOC 106 kb)
425_2015_2419_MOESM7_ESM.doc (44 kb)
Rubisco, leaf photosynthesis and senescence-related genes (DOC 43 kb)
425_2015_2419_MOESM8_ESM.docx (15 kb)
The overlap of meta-QTL reported by Xu et al. (2012) and in this study (DOCX 14 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Yijun Wang
    • 1
  • Jing Xu
    • 1
  • Dexiang Deng
    • 1
  • Haidong Ding
    • 2
  • Yunlong Bian
    • 1
  • Zhitong Yin
    • 1
  • Yarong Wu
    • 1
  • Bo Zhou
    • 1
  • Ye Zhao
    • 1
  1. 1.Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhouChina
  2. 2.College of Bioscience and BiotechnologyYangzhou UniversityYangzhouChina

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