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Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale

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Abstract

Key message

The genetic diversity and loci underlying agronomic traits were analyzed by the reads coverage and genome-wide association study based genotyping-by-sequencing in a diverse population consisting of 199 accessions.

Abstract

Triticale (× Triticosecale Wittmack) is an economically important grain forage and energy crop planted worldwide for its high biomass. Little is known about the genetic diversity and loci underlying agronomic traits in triticale. We performed genotyping-by-sequencing of 199 cultivars and mapped reads to the A, B, D, and R genomes for karyotype analysis. These cultivars could mostly be grouped into five types. Some chromosome abnormalities occurred with high frequency, such as 2D (2R) substitution, deletion of the long arm of chromosome 2D or the short arm of 5R, and translocation of the long arms of 7D/7A, the short arms of 6D/6A, or the long arms of 1D/1A. We chose only widely planted hexaploid triticale cultivars (153) for genome-wide association study. These cultivars could be divided into nine distinct groups, and the linkage disequilibrium decay was 25.4 kb in this population. We identified 253 significant marker-trait associations (MTAs) on 20 chromosomes, except 7R. Twenty-one reliable MTAs were identified repeatedly over two environments. We predicted 16 putative candidate genes involved in plant growth and development using the genome sequences of wheat and rye. These results provide a basis for understanding the genetic mechanisms of agronomic traits and will benefit the breeding of improved hexaploid triticale.

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Data availability

The datasets used and analyzed during the current study are available from the corresponding author upon reasonable request.

Abbreviations

GBS:

Genotyping-by-sequencing

GWAS:

Genome-wide association study

MTAs:

Marker-trait associations

PH:

Plant height

UIL:

Uppermost internode length

SL:

Spike length

SNS:

Spikelet number per spike

GNS:

Grain number per spike

SSP:

Seed setting percentage

TGW:

Thousand-grain weight

GL:

Grain length

GW:

Grain width

GA:

Grain area

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Funding

This research was financially supported by the QingHai Science and Technology Department (2019-ZJ-982Q), the National Natural Science Foundation of China (32160439).

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Authors and Affiliations

  1. Qinghai Province Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, People’s Republic of China

    Dong Cao, Shiming Li, Yun Li & Baolong Liu

  2. Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810008, People’s Republic of China

    Dong Cao, Shiming Li, Yun Li & Baolong Liu

  3. The Innovative Academy of Seed Design, Chinese Academy of Sciences, Xining, 810008, Qinghai, China

    Dong Cao, Yun Li & Baolong Liu

  4. University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China

    Dong Cao & Baolong Liu

  5. Department of Agriculture and Forestry, College of Agriculture and Animal Husbandry, Qinghai University, Qinghai, Xining, 810016, People’s Republic of China

    Dongxia Wang

  6. Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, People’s Republic of China

    Ming Hao

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  1. Dong Cao
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Contributions

DC and BL conceived and designed the experiments. DC, DW and MH performed the experiments, and SL analyzed the data. DC and BL wrote the paper. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Ming Hao or Baolong Liu.

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122_2022_4064_MOESM1_ESM.docx

Supplementary file1 Fig.S1: Chromosome constitutions of five ploidy species identified by fluorescent in situ hybridization (FISH). (a) Octaploid triticale (AABBDDRR), (b) hexaploid triticale (AABBRR), (c) hexaploid wheat (AABBDD), (d) tetraploid wheat (AABB), (e) rye (RR). Red FISH signals are from probe pSc119.2; Green signals are from probe pTa535 in a-d, while (AAC)5 in e. Fig.S2: Partial deletion of the short arm of chromosome 5R in triticale accessions based on read coverage. Fig.S3: Chromosomal translocations in triticale accessions based on read coverage. (a) Long arm of 7D/7A. (b) Short arm of 6D/6A. (c) Long arm of 1D/1A. Fig.S4: Insertion and deletion of seven chromosome segments in triticale accessions. Fig.S5: Distribution of 434,304 reliable SNPs used in genetic diversity analysis in the wheat and rye genomes. X-axis shows the position of SNPs on the chromosomes. Different colors represent the density of SNPs within a sliding window of 1 Mb. Fig.S6: Frequency distribution of 10 agronomic traits in 153 hexaploid triticale accessions. Fig.S7: Quantile-quantile (QQ) plots for ten agronomic traits. (DOCX 7773 kb)

122_2022_4064_MOESM2_ESM.xlsx

Supplementary file2 Table S1: Information on accessions used in this study. Table S2: Distribution of SNP markers on hexaploid triticale chromosomes. Table S3: Phenotypic variation of 10 agronomic traits over three environments. Table S4: Details of significant MTAs linked to 10 agronomic traits identified by GWAS and based on wheat and rye genome annotations. Table S5: Physical position comparison between the reported loci and MTAs identified in this study (XLSX 98 kb)

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Cao, D., Wang, D., Li, S. et al. Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale. Theor Appl Genet 135, 1705–1715 (2022). https://doi.org/10.1007/s00122-022-04064-5

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