Fine mapping and candidate gene analysis of a QTL associated with leaf rolling index on chromosome 4 of maize (Zea mays L.)

Gao, Lulu; Yang, Guanghui; Li, Yufeng; Fan, Nannan; Li, Hongjian; Zhang, Ming; Xu, Ruibin; Zhang, Mingyi; Zhao, Aiju; Ni, Zhongfu; Zhang, Yirong

doi:10.1007/s00122-019-03405-1

Original Article
Published: 09 August 2019

Fine mapping and candidate gene analysis of a QTL associated with leaf rolling index on chromosome 4 of maize (Zea mays L.)

Lulu Gao^1,2,
Guanghui Yang^1,2,
Yufeng Li^1,2,
Nannan Fan^1,5,
Hongjian Li^1,2,
Ming Zhang^1,2,
Ruibin Xu^1,2,
Mingyi Zhang³,
Aiju Zhao⁴,
Zhongfu Ni^1,2 &
Yirong Zhang^1,5

Theoretical and Applied Genetics volume 132, pages 3047–3062 (2019)Cite this article

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Abstract

Key message

One QTL qLRI4 controlling leaf rolling index on chromosome 4 was finely mapped, and ZmOCL5, a member of the HD-Zip class IV genes, is likely a candidate.

Abstract

Leaf rolling is an important agronomic trait related to plant architecture that can change the light condition and photosynthetic efficiency of the population. Here, we isolated one EMS-induced mutant in Chang7-2 background with extreme abaxial rolling leaf, named abrl1. Histological analysis showed that the increased number and area of bulliform cells may contribute to abaxial rolling leaf in abrl1. The F₂ and F_2:3 populations derived from Wu9086 with flat leaves and abrl1 were developed to map abrl1. Non-Mendelian segregation of phenotypic variation was observed in these populations and five genomic regions controlling the leaf rolling index (LRI) were identified, which could be due to the phenotypic difference between Chang7-2 and Wu9086. Moreover, one major QTL qLRI4 on chromosome 4 was further validated and finely mapped to a genetic interval between InDel13 and InDel10, with a physical distance of approximately 277 kb using NIL populations, among which one 602-bp insertion was identified in the promoter region of HD-Zip class IV gene Zm00001d049443 (named as ZmOCL5) of abrl1 compared with wild-type Chang7-2. Remarkably, the 602-bp InDel was associated with LRI in an F₂ population developed by crossing abrl1 mutant and its wild-type. In addition, the 602-bp insertion increased ZmOCL5 promoter activity and expression. Haplotype analysis demonstrated that the 602-bp insertion was a rare mutation event. Taken together, we propose that the rolled leaf in the abrl1 mutant may be partially attributed to the 602-bp insertion, which may be an attractive target for the genetic improvement of LRI in maize.

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Acknowledgements

This work was supported by the National Key Research and Development Program of China (2016YFD0101803) and the Ministry of Agriculture of China for Transgenic Research (2016ZX08009002).

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State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
Lulu Gao, Guanghui Yang, Yufeng Li, Nannan Fan, Hongjian Li, Ming Zhang, Ruibin Xu, Zhongfu Ni & Yirong Zhang
National Plant Gene Research Centre, Beijing, 100193, China
Lulu Gao, Guanghui Yang, Yufeng Li, Hongjian Li, Ming Zhang, Ruibin Xu & Zhongfu Ni
Dryland Agricultural Research Centre, Shanxi Academy of Agricultural Sciences, Taiyuan, 030031, China
Mingyi Zhang
Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Hebei Crop Genetic Breeding Laboratory, Shijiazhuang, 050035, China
Aiju Zhao
National Maize Improvement Centre of China, China Agricultural University, Beijing, China
Nannan Fan & Yirong Zhang

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Lulu Gao
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Guanghui Yang
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Yufeng Li
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Aiju Zhao
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Zhongfu Ni
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122_2019_3405_MOESM1_ESM.tif

Fig. S1 Characterization of the parental lines and F₁ morphology. a Mature plant. the bar represents 20 cm. b The ear leaf, ab abaxial. the bar represents 10 cm (TIFF 4698 kb)

Fig. S2 Histogram of the Wu9086/abrl1 F_2:3 families for leaf rolling index (LRI) (TIFF 1917 kb)

122_2019_3405_MOESM3_ESM.tif

Fig. S3 Gel electrophoresis of the amplification products using SSR markers. M-Marker; P1-Wu9086; P2-abrl1; F-Flat leaf bulk; R-Rolled-leaf bulk (TIFF 4514 kb)

122_2019_3405_MOESM4_ESM.tif

Fig. S4 Characterization of the 602-bp insertion sequence. a Schematic structure of the 602-bp insertion sequence. b Alignment of the 602-bp insertion sequence along with the 8 bp after the insertion site with the homologous sequences in the maize genome(B73_RefGen_v4.0). TSD, target-site duplications. A box and B box represent the predicted RNA polymerase III promoter regions (TIFF 9359 kb)

122_2019_3405_MOESM5_ESM.tif

Fig. S5 Characterization of NIL^Wu9086 and NIL^abrl1 morphology. a Morphology of NIL^Wu9086 and NIL^abrl1 at the mature period, bar = 20 cm. b Ear leaf morphology, ab abaxial, bar = 10 cm. c Transverse section of the widest part of the ear leaf, bar = 2 cm. d Morphology of male spike, bar = 2 cm (TIFF 4228 kb)

122_2019_3405_MOESM6_ESM.tif

Fig. S6 Comparison of LRIs of the ear leaf of NIL(B73)^B73 and NIL(B73)^abrl1 genotypes in BC₄F₂ populations of B73 background. NIL(B73)^B73 and NIL(B73)^abrl1 refers to the genotypes without 602-bp insertion and with homozygous 602-bp insertion, respectively. * indicates significance at the 0.05 level (Student’s t test) (TIFF 561 kb)

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Gao, L., Yang, G., Li, Y. et al. Fine mapping and candidate gene analysis of a QTL associated with leaf rolling index on chromosome 4 of maize (Zea mays L.). Theor Appl Genet 132, 3047–3062 (2019). https://doi.org/10.1007/s00122-019-03405-1

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Received: 21 March 2019
Accepted: 21 July 2019
Published: 09 August 2019
Issue Date: November 2019
DOI: https://doi.org/10.1007/s00122-019-03405-1

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Fig. S2 Histogram of the Wu9086/abrl1 F2:3 families for leaf rolling index (LRI) (TIFF 1917 kb)

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Fig. S2 Histogram of the Wu9086/abrl1 F_2:3 families for leaf rolling index (LRI) (TIFF 1917 kb)