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Cloning of TaSST genes associated with water soluble carbohydrate content in bread wheat stems and development of a functional marker

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Abstract

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We cloned TaSST genes, developed a gene-specific marker for TaSST - D1 , and identified three QTL in the Doumai/Shi 4185 RIL population. TaSST - D1 is within one of the three QTL.

Abstract

Sucrose:sucrose-1-fructosyltransferase (1-SST), a critical enzyme in the fructan biosynthetic pathway, is significantly and positively associated with water soluble carbohydrate (WSC) content in bread wheat stems. In the present study, wheat 1-SST genes (TaSST) were isolated and located on chromosomes 4A, 7A and 7D. Sequence analysis of TaSST-D1 revealed 15 single nucleotide polymorphisms (SNP) in the third exon between cultivars with higher and lower WSC content. A cleaved amplified polymorphism sequence (CAPS) marker, WSC7D, based on the polymorphism at position 1216 (C-G) was developed to discriminate the two alleles. WSC7D was located on chromosome 7DS using a recombinant inbred line (RIL) population from a Doumai/Shi 4185 cross, and a set of Chinese Spring nullisomic-tetrasomic lines. TaSST-D1 co-segregated with the CAPS marker WSC7D and was linked to SNP marker BS00108793_51 on chromosome 7DS at a genetic distance of 6.1 cM. It explained 8.8, 10.9, and 11.3 % of the phenotypic variances in trials at Beijing and Shijiazhuang as well as the averaged data from those environments, respectively. Two additional QTL (QWSC.caas-4BS and QWSC.caas-7AS) besides TaSST-D1 were mapped in the RIL population. One hundred and forty-nine Chinese wheat cultivars and advanced lines tested in four environments were used to validate a highly significant (P < 0.01) association between WSC7D and WSC content in wheat stems. WSC7D can be used as a gene-specific marker for improvement of stem WSC content in wheat breeding programs.

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Abbreviations

ANOVA:

Analysis of variance

CAPS:

Cleaved amplified polymorphism sequence

cDNA:

Complementary DNA

CS:

Chinese Spring

DPA:

Days post-anthesis

LOD:

Logarithm of odds

mRNA:

Messenger RNA

ORF:

Open reading frame

PCR:

Polymerase chain reaction

QTL:

Quantitative trait loci/locus

RIL:

Recombinant inbred line

SNP:

Single nucleotide polymorphism

TGW:

Thousand grain weight

WSC:

Water soluble carbohydrates

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Acknowledgments

We are grateful to Prof. R. A. McIntosh, Plant Breeding Institute, University of Sydney, for critical review of this manuscript. This study was supported by the National Natural Science Foundation of China (31201207, 31461143021), National 863 Project (2012AA10A308, 2012AA101105), International Science & Technology Cooperation Program of China (2014DFG31690), and China Agricultural Research System (CARS-3-1-3).

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Authors and Affiliations

  1. National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China

    Yan Dong, Yan Zhang, Yonggui Xiao, Jindong Liu, Yong Zhang, Ruilian Jing, Xianchun Xia & Zhonghu He

  2. Cotton Research Institute, CAAS, Huanghedadao, Anyang, Henan, China

    Jun Yan

  3. College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, 830052, Urumqi, Xinjiang, China

    Weie Wen

  4. International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, 100081, Beijing, China

    Zhonghu He

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  1. Yan Dong
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  2. Yan Zhang
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  3. Yonggui Xiao
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Correspondence to Xianchun Xia.

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Ethical standards

We declare that these experiments comply with the ethical standards in China, where they were performed.

Additional information

Communicated by I. D Godwin.

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Supplementary material 1 (DOCX 34 kb)

122_2016_2683_MOESM2_ESM.docx

Supplementary Figure S1 Frequency distributions of WSC content values in the Doumai/Shi 4185 RIL population. WSC content (%), A, Beijing; B, Shijiazhuang; C, The average. Mean values of the parents, Doumai and Shi 4185, are indicated by arrows. (DOCX 73 kb)

122_2016_2683_MOESM3_ESM.docx

Supplementary Figure S2 LOD contours obtained by inclusive composite interval mapping of QTL for WSC content in the Doumai/Shi 4185 RIL population. Beijing (purple line), Shijiazhuang (green line), and average (red line). LOD thresholds for declaring significant QTL were 2.0. (DOCX 64 kb)

122_2016_2683_MOESM4_ESM.docx

Supplementary Figure S3 PCR amplification of Chinese Spring nulli-tetrasomic lines with primer sets SST1 (a), SST2 (b), SST3 (c), SST4 (d), SST5 (e) and SST6 (f) used in this study. For example, no amplification was observed in N4A-T4B, whereas the fragment was generated in other nulli-tetrasomics, indicating that the TaSST gene was located on wheat chromosome 4A. M DL2000, 01 N1A-T1B, 02 N1B-T1D, 03 N1D-T1A, 04 M2A-T2D, 05 N2B-T2A, 06 N2D-T2B, 07 N3A-T3B, 08 N3B-T3D, 09 N3D-T3A, 10 N4A-T4B, 11 N4B-T4D, 12 N4D-T4A, 13 N5A-T5B, 14 N5B-T5D, 15 N5D-T5A, 16 N6A-T6B, 17 N6B-T6D, 18 N6D-T6A,19 N7A-T7B,20 N7B-T7D, 21 N7D-T7A. (DOCX 207 kb)

122_2016_2683_MOESM5_ESM.docx

Supplementary Figure S4 PCR amplification of Chinese Spring nulli-tetrasomic lines and ditelosomic lines 7DS with the marker WSC7D. M DL2000, 01 N1A-T1B, 02 N1B-T1D, 03 N1D-T1A, 04 M2A-T2D, 05 N2B-T2A, 06 N2D-T2B, 07 N3A-T3B, 08 N3B-T3D, 09 N3D-T3A, 10 N4A-T4B, 11 N4B-T4D, 12 N4D-T4A, 13 N5A-T5B, 14 N5B-T5D, 15 N5D-T5A, 16 N6A-T6B, 17 N6B-T6D, 18 N6D-T6A, 19 N7A-T7B, 20 N7B-T7D, 21 N7D-T7A, 22 DT7DS. (DOCX 45 kb)

122_2016_2683_MOESM6_ESM.docx

Supplementary Figure S5 Schematic representation of the exon–intron structures of the TaSST-A1, TaSST-A2 and TaSST-D1. The black arrows indicate exons, the lines represent introns, and numbers indicate their sizes (bp). (DOCX 31 kb)

122_2016_2683_MOESM7_ESM.docx

Supplementary Figure S6 DNA sequences of TaSST-A2 for eight cultivars. Nucleotides relative to the translational start site (0) are numbered. SNPs or InDels among the eight cultivars are shown in red or green color. The allele with 13-bp insertion in the third intron was designated as TaSST-A2b (KU376265) and the other as TaSST-A2a (KU376264). (DOCX 797 kb)

122_2016_2683_MOESM8_ESM.docx

Supplementary Figure S7 DNA sequences of TaSST-D1 for eight cultivars. Nucleotides relative to the translational start site (0) are numbered. SNPs among the eight cultivars are shown in red or green color. The alleles in four cultivars with higher and four with lower WSC content were designated as TaSST-D1a (KU376266) and TaSST-D1b (KU376267), respectively. (DOCX 766 kb)

122_2016_2683_MOESM9_ESM.docx

Supplementary Figure S8 Test of polymorphism of CAPS marker WSC7D in Chinese wheat cultivars. The 7D genome-specific primer set WSC7D was used firstly to amplify a 770 bp fragment from all cultivars (a). The PCR product was then digested with SacI; a 633 bp band was obtained in the genotype TaSST-D1a and a 770 bp was produced in TaSST-D1b lines (b). M DL2000; 01 Guan 35 (20.6 %); 02 11CA40 (20.6 %); 03 Zhoumai 30 (20.8 %); 04 Huaimai 20 (21.3 %); 05 Yumai 21 (21.6 %); 06 Neixiang 188 (22.4 %); Bima 4 (7.8 %); 08 Abbondanza (9.6 %); 09 Aifeng 3 (10.4 %); 10 Zhengzhou 3 (11.0 %); 11 Gaocheng 8901 (11.2 %); 12 Xinong 291 (12.0 %). (DOCX 58 kb)

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Dong, Y., Zhang, Y., Xiao, Y. et al. Cloning of TaSST genes associated with water soluble carbohydrate content in bread wheat stems and development of a functional marker. Theor Appl Genet 129, 1061–1070 (2016). https://doi.org/10.1007/s00122-016-2683-5

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