Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa

Abstract Common bean (Phaseolus vulgaris L.) is important in African diets for protein, iron (Fe), and zinc (Zn), but traditional cultivars have long cooking time (CKT), which increases the time, energy, and health costs of cooking. Genomic selection was used to predict genomic estimated breeding va...

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Autores principales:	Renu Saradadevi, Clare Mukankusi, Li Li, Winnyfred Amongi, Julius Peter Mbiu, Bodo Raatz, Daniel Ariza, Steve Beebe, Rajeev K. Varshney, Eric Huttner, Brian Kinghorn, Robert Banks, Jean Claude Rubyogo, Kadambot H. M. Siddique, Wallace A. Cowling
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	Plant culture SB1-1110 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/63771bfe87d548ce940cbc8ec7888e9f
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spelling	oai:doaj.org-article:63771bfe87d548ce940cbc8ec7888e9f2021-12-05T07:50:11ZMultivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa1940-337210.1002/tpg2.20156https://doaj.org/article/63771bfe87d548ce940cbc8ec7888e9f2021-11-01T00:00:00Zhttps://doi.org/10.1002/tpg2.20156https://doaj.org/toc/1940-3372Abstract Common bean (Phaseolus vulgaris L.) is important in African diets for protein, iron (Fe), and zinc (Zn), but traditional cultivars have long cooking time (CKT), which increases the time, energy, and health costs of cooking. Genomic selection was used to predict genomic estimated breeding values (GEBV) for grain yield (GY), CKT, Fe, and Zn in an African bean panel of 358 genotypes in a two‐stage analysis. In Stage 1, best linear unbiased estimates (BLUE) for each trait were obtained from 898 genotypes across 33 field trials in East Africa. In Stage 2, BLUE in a training population of 141 genotypes were used in a multivariate genomic analysis with genome‐wide single nucleotide polymorphism data from the African bean panel. Moderate to high genomic heritability was found for GY (0.45 ± 0.10), CKT (0.50 ± 0.15), Fe (0.57 ± 0.12), and Zn (0.61 ± 0.13). There were significant favorable genetic correlations between Fe and Zn (0.91 ± 0.06), GY and Fe (0.66 ± 0.17), GY and Zn (0.44 ± 0.19), CKT and Fe (−0.57 ± 0.21), and CKT and Zn (−0.67 ± 0.20). Optimal contributions selection (OCS), based on economic index of weighted GEBV for each trait, was used to design crossing within four market groups relevant to East Africa. Progeny were predicted by OCS to increase in mean GY by 12.4%, decrease in mean CKT by 9.3%, and increase in mean Fe and Zn content by 6.9 and 4.6%, respectively, with low achieved coancestry of 0.032. Genomic selection with OCS will accelerate breeding of high‐yielding, biofortified, and rapid cooking African common bean cultivars.Renu SaradadeviClare MukankusiLi LiWinnyfred AmongiJulius Peter MbiuBodo RaatzDaniel ArizaSteve BeebeRajeev K. VarshneyEric HuttnerBrian KinghornRobert BanksJean Claude RubyogoKadambot H. M. SiddiqueWallace A. CowlingWileyarticlePlant cultureSB1-1110GeneticsQH426-470ENThe Plant Genome, Vol 14, Iss 3, Pp n/a-n/a (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Plant culture SB1-1110 Genetics QH426-470
spellingShingle	Plant culture SB1-1110 Genetics QH426-470 Renu Saradadevi Clare Mukankusi Li Li Winnyfred Amongi Julius Peter Mbiu Bodo Raatz Daniel Ariza Steve Beebe Rajeev K. Varshney Eric Huttner Brian Kinghorn Robert Banks Jean Claude Rubyogo Kadambot H. M. Siddique Wallace A. Cowling Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa
description	Abstract Common bean (Phaseolus vulgaris L.) is important in African diets for protein, iron (Fe), and zinc (Zn), but traditional cultivars have long cooking time (CKT), which increases the time, energy, and health costs of cooking. Genomic selection was used to predict genomic estimated breeding values (GEBV) for grain yield (GY), CKT, Fe, and Zn in an African bean panel of 358 genotypes in a two‐stage analysis. In Stage 1, best linear unbiased estimates (BLUE) for each trait were obtained from 898 genotypes across 33 field trials in East Africa. In Stage 2, BLUE in a training population of 141 genotypes were used in a multivariate genomic analysis with genome‐wide single nucleotide polymorphism data from the African bean panel. Moderate to high genomic heritability was found for GY (0.45 ± 0.10), CKT (0.50 ± 0.15), Fe (0.57 ± 0.12), and Zn (0.61 ± 0.13). There were significant favorable genetic correlations between Fe and Zn (0.91 ± 0.06), GY and Fe (0.66 ± 0.17), GY and Zn (0.44 ± 0.19), CKT and Fe (−0.57 ± 0.21), and CKT and Zn (−0.67 ± 0.20). Optimal contributions selection (OCS), based on economic index of weighted GEBV for each trait, was used to design crossing within four market groups relevant to East Africa. Progeny were predicted by OCS to increase in mean GY by 12.4%, decrease in mean CKT by 9.3%, and increase in mean Fe and Zn content by 6.9 and 4.6%, respectively, with low achieved coancestry of 0.032. Genomic selection with OCS will accelerate breeding of high‐yielding, biofortified, and rapid cooking African common bean cultivars.
format	article
author	Renu Saradadevi Clare Mukankusi Li Li Winnyfred Amongi Julius Peter Mbiu Bodo Raatz Daniel Ariza Steve Beebe Rajeev K. Varshney Eric Huttner Brian Kinghorn Robert Banks Jean Claude Rubyogo Kadambot H. M. Siddique Wallace A. Cowling
author_facet	Renu Saradadevi Clare Mukankusi Li Li Winnyfred Amongi Julius Peter Mbiu Bodo Raatz Daniel Ariza Steve Beebe Rajeev K. Varshney Eric Huttner Brian Kinghorn Robert Banks Jean Claude Rubyogo Kadambot H. M. Siddique Wallace A. Cowling
author_sort	Renu Saradadevi
title	Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa
title_short	Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa
title_full	Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa
title_fullStr	Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa
title_full_unstemmed	Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa
title_sort	multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in east africa
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/63771bfe87d548ce940cbc8ec7888e9f
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Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa

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