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Structural variation in the 5′ upstream region of photoperiod-insensitive alleles Ppd-A1a and Ppd-B1a identified in hexaploid wheat (Triticum aestivum L.), and their effect on heading time

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Abstract

For genetic analysis of Ppd-1 homoeologs controlling photoperiodic response of wheat (Triticum aestivum L.), bulk segregant analysis was performed using a doubled haploid (DH) population derived from a cross of Japanese wheat genotypes Winter-Abukumawase and Chihokukomugi. Based on the segregation of simple sequence repeat markers linked to the Ppd-1 homoeologs, Winter-Abukumawase carried insensitive alleles Ppd-B1a and Ppd-D1a and Chihokukomugi carried a single insensitive allele (Ppd-A1a) that was first found in common wheat. The genomic sequence of Ppd-1 homoeologs including the 5′ upstream region was determined and compared between the two genotypes. Ppd-D1a of Winter-Abukumawase had a deletion of 2,089 bp that was already reported for Ciano 67. Critical sequence polymorphism causing photoperiod insensitivity was not detected from the translation start codon to the 3′ untranslated region of Ppd-A1 and Ppd-B1. However, novel mutations were found in the 5′ upstream region. Ppd-A1a of Chihokukomugi had a deletion of 1,085 bp and Ppd-B1a of Winter-Abukumawase had an insertion of 308 bp. A total of 80 DH lines were classified into eight genotypes by PCR-based genotyping using specific primer sets to detect the In/Dels in the 5′ upstream region of three Ppd-1 genes. The heading dates of the DH lines differed significantly between the eight genotypes, showing that each of the three insensitive alleles accelerates heading by 7–9 days compared with the photoperiod-sensitive genotype. Interaction between the three genes was also significant.

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Acknowledgments

This study was partly supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Green Technology Project GD-3005) and the Japan Society for the Promotion of Science (JSPS) Asian CORE Program entitled “Cooperative Research and Educational Center for Important Plant Genetic Resources in East Asia”.

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Authors and Affiliations

  1. Graduate School of Environmental and Life Science, Okayama University, 1-1-1, Tsushima-Naka, Kita-Ku, Okayama, 700-0011, Japan

    Hidetaka Nishida, Tetsuya Yoshida, Kohei Kawakami, Yukari Akashi & Kenji Kato

  2. National Agricultural Research Center for Kyushu Okinawa Region, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan

    Masaya Fujita

  3. Faculty of Life Science, Yunnan University, 2 North Cuihu Lake Road, Kunming, 650091, China

    Bo Long

  4. Crop Genetics Department, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK

    David A. Laurie

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  1. Hidetaka Nishida
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  2. Tetsuya Yoshida
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  3. Kohei Kawakami
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  4. Masaya Fujita
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  5. Bo Long
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  6. Yukari Akashi
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  7. David A. Laurie
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  8. Kenji Kato
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Correspondence to Kenji Kato.

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11032_2012_9765_MOESM2_ESM.ppt

Supplementary Fig. S1 PCR assays to identify the Ppd-1 genotype of cultivars Winter-Abukumawase (W-AB), Chihokukomugi (CK), Chinese Spring (CS) and Haruhikari (HH), using diagnostic PCR primers shown in Supplementary Table S1 and Fig. 2. a Ppd-A1a.1 allele of CK (338-bp) is clearly distinguished by multiplex PCR to amplify the 5′ upstream region of Ppd-A1. b Ppd-B1a.1 allele of W-AB (620 bp) is clearly distinguished by amplifying the 5′ upstream region of Ppd-B1. c Ppd-D1a.1 allele of W-AB (415 bp) is clearly distinguished by multiplex PCR to amplify the 5′ upstream region of Ppd-D1. M 100-bp DNA ladder (PDF 51 kb)

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Nishida, H., Yoshida, T., Kawakami, K. et al. Structural variation in the 5′ upstream region of photoperiod-insensitive alleles Ppd-A1a and Ppd-B1a identified in hexaploid wheat (Triticum aestivum L.), and their effect on heading time. Mol Breeding 31, 27–37 (2013). https://doi.org/10.1007/s11032-012-9765-0

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