Breeding for dual-purpose wheat varieties using marker–trait associations for biomass yield and quality traits

Pernille Louise Malik; Luc Janss; Finn Borum; Henning Jørgensen; Birger Eriksen; Jan K. Schjoerring; Søren Kjærsgaard Rasmussen

doi:10.1007/s00122-019-03431-z

Breeding for dual-purpose wheat varieties using marker–trait associations for biomass yield and quality traits

Pernille Louise Malik, Luc Janss, Finn Borum, Henning Jørgensen, Birger Eriksen, Jan K. Schjoerring, Søren Kjærsgaard Rasmussen

Section for Plant and Soil Sciences

3 Citations (Scopus)

9 Downloads (Pure)

Abstract

Key message: This study demonstrates that an active breeding nursery with rotation can be used to identify marker–trait associations for biomass yield and quality parameters that are important for biorefinery purposes. Abstract: Wheat straw is a valuable feedstock for bioethanol production, but due to the recalcitrant nature of lignocellulose, its efficient use in biorefineries is limited by its low digestibility and difficult conversion of structural carbohydrates into free sugars. A genome-wide association study (GWAS) was conducted to search for significant SNP markers that could be used in a breeding programme to improve the value of wheat straw in a biorefinery setting. As part of a 3-year breeding programme (2013–2016), 190 winter wheat lines were phenotyped for traits that affect the yield and quality of the harvested biomass. These traits included straw yield, plant height, lodging at three growth stages and Septoria tritici blotch (STB) susceptibility. Release of glucose, xylose and arabinose was determined after hydrothermal pretreatment and enzymatic hydrolysis of the straw. The lines were genotyped using 15 K SNP markers and 5552 SNP markers could be used after filtering. Heritability for all traits ranged from 0.02 to 0.74. GWASs were conducted using CMLM, SUPER and FarmCPU algorithms, to analyse which algorithm could detect the highest number of marker–trait associations (MTAs). Comparable tendencies were obtained from CMLM and FarmCPU, but FarmCPU produced the most significant results. MTAs were obtained for lodging, harvest index, plant height, STB, glucose, xylose and arabinose at a significance level of p < 9.01 × 10⁻⁶. MTAs in chromosome 6A were observed for glucose, xylose and arabinose, and could be of importance for increasing sugar release for bioethanol production.

Original language	English
Journal	Theoretical and Applied Genetics
Volume	132
Pages (from-to)	3375-3398
ISSN	0040-5752
DOIs	https://doi.org/10.1007/s00122-019-03431-z
Publication status	Published - 1 Dec 2019

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title = "Breeding for dual-purpose wheat varieties using marker–trait associations for biomass yield and quality traits",

abstract = "Key message: This study demonstrates that an active breeding nursery with rotation can be used to identify marker–trait associations for biomass yield and quality parameters that are important for biorefinery purposes. Abstract: Wheat straw is a valuable feedstock for bioethanol production, but due to the recalcitrant nature of lignocellulose, its efficient use in biorefineries is limited by its low digestibility and difficult conversion of structural carbohydrates into free sugars. A genome-wide association study (GWAS) was conducted to search for significant SNP markers that could be used in a breeding programme to improve the value of wheat straw in a biorefinery setting. As part of a 3-year breeding programme (2013–2016), 190 winter wheat lines were phenotyped for traits that affect the yield and quality of the harvested biomass. These traits included straw yield, plant height, lodging at three growth stages and Septoria tritici blotch (STB) susceptibility. Release of glucose, xylose and arabinose was determined after hydrothermal pretreatment and enzymatic hydrolysis of the straw. The lines were genotyped using 15 K SNP markers and 5552 SNP markers could be used after filtering. Heritability for all traits ranged from 0.02 to 0.74. GWASs were conducted using CMLM, SUPER and FarmCPU algorithms, to analyse which algorithm could detect the highest number of marker–trait associations (MTAs). Comparable tendencies were obtained from CMLM and FarmCPU, but FarmCPU produced the most significant results. MTAs were obtained for lodging, harvest index, plant height, STB, glucose, xylose and arabinose at a significance level of p < 9.01 × 10−6. MTAs in chromosome 6A were observed for glucose, xylose and arabinose, and could be of importance for increasing sugar release for bioethanol production.",

author = "Malik, {Pernille Louise} and Luc Janss and Finn Borum and Henning J{\o}rgensen and Birger Eriksen and Schjoerring, {Jan K.} and Rasmussen, {S{\o}ren Kj{\ae}rsgaard}",

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language = "English",

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T1 - Breeding for dual-purpose wheat varieties using marker–trait associations for biomass yield and quality traits

AU - Malik, Pernille Louise

AU - Janss, Luc

AU - Borum, Finn

AU - Jørgensen, Henning

AU - Eriksen, Birger

AU - Schjoerring, Jan K.

AU - Rasmussen, Søren Kjærsgaard

PY - 2019/12/1

Y1 - 2019/12/1

N2 - Key message: This study demonstrates that an active breeding nursery with rotation can be used to identify marker–trait associations for biomass yield and quality parameters that are important for biorefinery purposes. Abstract: Wheat straw is a valuable feedstock for bioethanol production, but due to the recalcitrant nature of lignocellulose, its efficient use in biorefineries is limited by its low digestibility and difficult conversion of structural carbohydrates into free sugars. A genome-wide association study (GWAS) was conducted to search for significant SNP markers that could be used in a breeding programme to improve the value of wheat straw in a biorefinery setting. As part of a 3-year breeding programme (2013–2016), 190 winter wheat lines were phenotyped for traits that affect the yield and quality of the harvested biomass. These traits included straw yield, plant height, lodging at three growth stages and Septoria tritici blotch (STB) susceptibility. Release of glucose, xylose and arabinose was determined after hydrothermal pretreatment and enzymatic hydrolysis of the straw. The lines were genotyped using 15 K SNP markers and 5552 SNP markers could be used after filtering. Heritability for all traits ranged from 0.02 to 0.74. GWASs were conducted using CMLM, SUPER and FarmCPU algorithms, to analyse which algorithm could detect the highest number of marker–trait associations (MTAs). Comparable tendencies were obtained from CMLM and FarmCPU, but FarmCPU produced the most significant results. MTAs were obtained for lodging, harvest index, plant height, STB, glucose, xylose and arabinose at a significance level of p < 9.01 × 10−6. MTAs in chromosome 6A were observed for glucose, xylose and arabinose, and could be of importance for increasing sugar release for bioethanol production.

AB - Key message: This study demonstrates that an active breeding nursery with rotation can be used to identify marker–trait associations for biomass yield and quality parameters that are important for biorefinery purposes. Abstract: Wheat straw is a valuable feedstock for bioethanol production, but due to the recalcitrant nature of lignocellulose, its efficient use in biorefineries is limited by its low digestibility and difficult conversion of structural carbohydrates into free sugars. A genome-wide association study (GWAS) was conducted to search for significant SNP markers that could be used in a breeding programme to improve the value of wheat straw in a biorefinery setting. As part of a 3-year breeding programme (2013–2016), 190 winter wheat lines were phenotyped for traits that affect the yield and quality of the harvested biomass. These traits included straw yield, plant height, lodging at three growth stages and Septoria tritici blotch (STB) susceptibility. Release of glucose, xylose and arabinose was determined after hydrothermal pretreatment and enzymatic hydrolysis of the straw. The lines were genotyped using 15 K SNP markers and 5552 SNP markers could be used after filtering. Heritability for all traits ranged from 0.02 to 0.74. GWASs were conducted using CMLM, SUPER and FarmCPU algorithms, to analyse which algorithm could detect the highest number of marker–trait associations (MTAs). Comparable tendencies were obtained from CMLM and FarmCPU, but FarmCPU produced the most significant results. MTAs were obtained for lodging, harvest index, plant height, STB, glucose, xylose and arabinose at a significance level of p < 9.01 × 10−6. MTAs in chromosome 6A were observed for glucose, xylose and arabinose, and could be of importance for increasing sugar release for bioethanol production.

U2 - 10.1007/s00122-019-03431-z

DO - 10.1007/s00122-019-03431-z

M3 - Journal article

C2 - 31555887

SN - 0040-5752

VL - 132

SP - 3375

EP - 3398

JO - Theoretical and Applied Genetics

JF - Theoretical and Applied Genetics

ER -

Breeding for dual-purpose wheat varieties using marker–trait associations for biomass yield and quality traits

Abstract

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