<i>De novo</i> QTL-seq Identifies Loci Linked to Blanchability in Peanut (<i>Arachis hypogaea</i>) and Refines Previously Identified QTL with Low Coverage Sequence

Blanchability is an often overlooked, but important trait for peanut breeding. The process of blanching, removing the skin, is an important step in the processing of raw nuts for manufacturing. Under strong genetic control and requiring considerable effort to phenotype, blanchability is conducive fo...

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Autores principales:	Walid Korani, Dan O’Connor, Ye Chu, Carolina Chavarro, Carolina Ballen, Baozhu Guo, Peggy Ozias-Akins, Graeme Wright, Josh Clevenger
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	blanchability QTL-seq polyploid Agriculture S
Acceso en línea:	https://doaj.org/article/800ffa40132140989dc3939e77d944f1
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spelling	oai:doaj.org-article:800ffa40132140989dc3939e77d944f12021-11-25T16:06:31Z<i>De novo</i> QTL-seq Identifies Loci Linked to Blanchability in Peanut (<i>Arachis hypogaea</i>) and Refines Previously Identified QTL with Low Coverage Sequence10.3390/agronomy111122012073-4395https://doaj.org/article/800ffa40132140989dc3939e77d944f12021-10-01T00:00:00Zhttps://www.mdpi.com/2073-4395/11/11/2201https://doaj.org/toc/2073-4395Blanchability is an often overlooked, but important trait for peanut breeding. The process of blanching, removing the skin, is an important step in the processing of raw nuts for manufacturing. Under strong genetic control and requiring considerable effort to phenotype, blanchability is conducive for marker-assisted selection. We used QTL sequencing (QTL-seq) to identify two QTLs related to blanchability using previously phenotyped breeding populations. To validate the QTLs, we show that two markers can select for significantly increased blanchability in an independent recombinant inbred line (RIL) population. Two wild introgressions from <i>Arachis cardenasii</i> conferring strong disease resistance were segregated in the population and were found to negatively impact blanchability. Finally, we show that by utilizing highly accurate sequence analysis pipelines, low coverage sequencing can be used to genotype whole populations with increased power and precision. This study highlights the potential to mine breeding data to identify and develop useful markers for genetic improvement programs, and provide powerful tools for breeding for processing and quality traits.Walid KoraniDan O’ConnorYe ChuCarolina ChavarroCarolina BallenBaozhu GuoPeggy Ozias-AkinsGraeme WrightJosh ClevengerMDPI AGarticleblanchabilityQTL-seqpolyploidAgricultureSENAgronomy, Vol 11, Iss 2201, p 2201 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	blanchability QTL-seq polyploid Agriculture S
spellingShingle	blanchability QTL-seq polyploid Agriculture S Walid Korani Dan O’Connor Ye Chu Carolina Chavarro Carolina Ballen Baozhu Guo Peggy Ozias-Akins Graeme Wright Josh Clevenger <i>De novo</i> QTL-seq Identifies Loci Linked to Blanchability in Peanut (<i>Arachis hypogaea</i>) and Refines Previously Identified QTL with Low Coverage Sequence
description	Blanchability is an often overlooked, but important trait for peanut breeding. The process of blanching, removing the skin, is an important step in the processing of raw nuts for manufacturing. Under strong genetic control and requiring considerable effort to phenotype, blanchability is conducive for marker-assisted selection. We used QTL sequencing (QTL-seq) to identify two QTLs related to blanchability using previously phenotyped breeding populations. To validate the QTLs, we show that two markers can select for significantly increased blanchability in an independent recombinant inbred line (RIL) population. Two wild introgressions from <i>Arachis cardenasii</i> conferring strong disease resistance were segregated in the population and were found to negatively impact blanchability. Finally, we show that by utilizing highly accurate sequence analysis pipelines, low coverage sequencing can be used to genotype whole populations with increased power and precision. This study highlights the potential to mine breeding data to identify and develop useful markers for genetic improvement programs, and provide powerful tools for breeding for processing and quality traits.
format	article
author	Walid Korani Dan O’Connor Ye Chu Carolina Chavarro Carolina Ballen Baozhu Guo Peggy Ozias-Akins Graeme Wright Josh Clevenger
author_facet	Walid Korani Dan O’Connor Ye Chu Carolina Chavarro Carolina Ballen Baozhu Guo Peggy Ozias-Akins Graeme Wright Josh Clevenger
author_sort	Walid Korani
title	<i>De novo</i> QTL-seq Identifies Loci Linked to Blanchability in Peanut (<i>Arachis hypogaea</i>) and Refines Previously Identified QTL with Low Coverage Sequence
title_short	<i>De novo</i> QTL-seq Identifies Loci Linked to Blanchability in Peanut (<i>Arachis hypogaea</i>) and Refines Previously Identified QTL with Low Coverage Sequence
title_full	<i>De novo</i> QTL-seq Identifies Loci Linked to Blanchability in Peanut (<i>Arachis hypogaea</i>) and Refines Previously Identified QTL with Low Coverage Sequence
title_fullStr	<i>De novo</i> QTL-seq Identifies Loci Linked to Blanchability in Peanut (<i>Arachis hypogaea</i>) and Refines Previously Identified QTL with Low Coverage Sequence
title_full_unstemmed	<i>De novo</i> QTL-seq Identifies Loci Linked to Blanchability in Peanut (<i>Arachis hypogaea</i>) and Refines Previously Identified QTL with Low Coverage Sequence
title_sort	<i>de novo</i> qtl-seq identifies loci linked to blanchability in peanut (<i>arachis hypogaea</i>) and refines previously identified qtl with low coverage sequence
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/800ffa40132140989dc3939e77d944f1
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<i>De novo</i> QTL-seq Identifies Loci Linked to Blanchability in Peanut (<i>Arachis hypogaea</i>) and Refines Previously Identified QTL with Low Coverage Sequence

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