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QTL mapping and analysis of epistatic interactions for grain yield and yield-related traits in Triticum turgidum L. var. durum

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Abstract

A quantitative trait loci (QTL) analysis of grain yield and yield-related traits was performed on 93 durum wheat recombinant inbred lines derived from the cross UC1113 × Kofa. The mapping population and parental lines were analyzed considering 19 traits assessed in different Argentine environments, namely grain yield, heading date, flowering time, plant height, biomass per plant, and spikelet number per ear, among others. A total of 224 QTL with logarithm of odds ratio (LOD) ≥ 3 and 47 additional QTL with LOD > 2.0 were detected. These QTL were clustered in 35 regions with overlapping QTL, and 12 genomic regions were associated with only one phenotypic trait. The regions with the highest number of multi-trait and stable QTL were 3BS.1, 3BS.2, 2BS.1, 1BL.1, 3AL.1, 1AS, and 4AL.3. The effects of epistatic QTL and QTL × environment interactions were also analyzed. QTL putatively located at major gene loci (Rht, Vrn, Eps, and Ppd) as well as additional major/minor QTL involved in the complex genetic basis of yield-related traits expressed in Argentine environments were identified. Interestingly, the 3AL.1 region was found to increase yield without altering grain quality or crop phenology.

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Abbreviations

QTL:

Quantitative trait locus

RIL:

Recombinant inbred line

Rht:

Reduced height

MAS:

Marker assisted selection

NDVI:

Normalized difference vegetation index

Ppd:

Photoperiod

Vrn:

Vernalization

Eps:

Earliness per se

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

RFLP:

Restriction fragment length polymorphism

STS:

Sequence-tagged site

CA:

Cabildo

BW:

Barrow

BC:

Balcarce

Hd:

Heading date

Flt:

Flowering time

Ssm:

Number of spikes per square meter

Yld:

Grain yield

Tgw:

Thousand grain weight

Ph:

Plant height

PdL:

Peduncle length

Bpp:

Biomass per plant

Snp:

Number of spikes per plant

Gne:

Grain number per ear

Gnp:

Grain number per plant

Sne:

Spikelet number per ear

Fse:

Number of fertile spikelets per ear

Gwe:

Grain weight per ear

Gwp:

Grain weight per plant

Gnfs:

Grain number per fertile spikelet

Gnts:

Grain number per total spikelets

Hi:

Harvest index

Sf:

Spike fertility

QQ:

Epistatic interaction

QE:

QTL × environment interaction

LOD:

Logarithm of odds ratio

Ypc:

Yellow pigment content

Fb:

Flour yellow color (b CIELAB)

Gpc:

Grain protein content

Sv:

Sedimentation volume (SDS test)

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Acknowledgements

We gratefully acknowledge Dr. Jorge Dubcovsky for providing the molecular map and mapping population to carry out the present analysis. We thank the Asociación de Cooperativas Argentinas, INTA EEA Barrow, EEA Balcarce, and EEA Marcos Juárez represented by Ing. Rubén Miranda, Ing. Carlos Jensen, Ing. Horacio Bariffi, and Ing. Beatriz Formica, respectively, for providing the experimental fields and sowing the field trials. We also thank Ing. Patricia Gómez for her technical support. We gratefully acknowledge Dr Robert McIntosh by their carefully review of the manuscript. This project was financed by the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional del Sur (UNS, PGI TIR 24/A185, and 24/TA11), and Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT: PICT 1011, PAE 37108, and PICT 0660).

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Author notes

  1. Pablo F. Roncallo and Pavan C. Akkiraju contributed equally to the article.

Authors and Affiliations

  1. Laboratorio de Biotecnología Vegetal, CERZOS-CONICET/UNS, CCT Bahía Blanca, Camino de la Carrindanga km 7, 8000, Bahía Blanca, Argentina

    Pablo F. Roncallo, Pavan C. Akkiraju & Viviana C. Echenique

  2. Departamento de Agronomía, Universidad Nacional del Sur, San Andrés 800, 8000, Bahía Blanca, Argentina

    Pablo F. Roncallo, Pavan C. Akkiraju & Viviana C. Echenique

  3. CEFOBI-CONICET, Suipacha 531, S2002 LRK, Rosario, Argentina

    Gerardo L. Cervigni

Authors
  1. Pablo F. Roncallo
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  2. Pavan C. Akkiraju
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  3. Gerardo L. Cervigni
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  4. Viviana C. Echenique
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Corresponding author

Correspondence to Viviana C. Echenique.

Electronic supplementary material

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Supplementary material 1 (DOCX 23 kb)

Supplementary material 2 (DOCX 46 kb)

Supplementary material 3 (DOCX 72 kb)

Supplementary material 4 (DOCX 111 kb)

Supplementary material 5 (DOCX 20 kb)

Supplementary material 6 (DOCX 29 kb)

Supplementary material 7 (PDF 288 kb)

QTL associated with yield and yield-related traits mapped on chromosomes 2A, 4A, 4B, 5A, 5B, 6A, 6B, 7A, and 7B using UC1113 × Kofa RIL mapping population. Bars represent QTL confidence intervals with 2-LOD drop offs; QTL and environment are indicated at the top. Centromeres are indicated by grey squares. Peak positions are indicated by horizontal lines within QTL bars. Major genes Rht-B1, Rht-A1, Rht9, and Rht12 are indicated on the map, according to the positions reported by Ellis et al. (2005) and Wilhelm et al. (2013). The genetic map was adapted from Zhang et al. (2008)

Supplementary material 8 (PDF 479 kb)

QTL mapping results obtained using multiple trait mapping for clusters located on chromosomes 1A and 1B. Each graph represents chromosome distance in cM (x axis) and LOD score value (y axis)

Supplementary material 9 (PDF 85 kb)

QTL mapping results obtained using multiple trait mapping for the clusters located on chromosomes 2B. Each graph represents chromosome distance in cM (x axis) and LOD score value (y axis)

Supplementary material 10 (PDF 143 kb)

QTL mapping results obtained using multiple trait mapping for the clusters located on chromosomes 3A and 3B. Each graph represents chromosome distance in cM (x axis) and LOD score value (y axis)

Supplementary material 11 (PDF 121 kb)

QTL mapping results obtained using multiple trait mapping for the clusters located on chromosomes 4A and 4B. Each graph represents chromosome distance in cM (x axis) and LOD score value (y axis)

Supplementary material 12 (PDF 87 kb)

QTL mapping results obtained using multiple trait mapping for the clusters located on chromosomes 5A. Each graph represents chromosome distance in cM (x axis) and LOD score value (y axis)

Supplementary material 13 (PDF 67 kb)

QTL mapping results obtained using multiple trait mapping for the clusters located on chromosomes 6A and 6B. Each graph represents chromosome distance in cM (x axis) and LOD score value (y axis)

Supplementary material 14 (PDF 278 kb)

QTL mapping results obtained using multiple trait mapping for the clusters located on chromosomes 7A and 7B. Each graph represents chromosome distance in cM (x axis) and LOD score value (y axis)

Supplementary material 15 (DOCX 37 kb)

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Roncallo, P.F., Akkiraju, P.C., Cervigni, G.L. et al. QTL mapping and analysis of epistatic interactions for grain yield and yield-related traits in Triticum turgidum L. var. durum . Euphytica 213, 277 (2017). https://doi.org/10.1007/s10681-017-2058-2

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