Using phenomics to identify and integrate traits of interest for better-performing common beans: A validation study on an interspecific hybrid and its Acutifolii parents
IntroductionEvaluations of interspecific hybrids are limited, as classical genebank accession descriptors are semi-subjective, have qualitative traits and show complications when evaluating intermediate accessions. However, descriptors can be quantified using recognized phenomic traits. This digital...
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1008666/full |
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| author | Diego Felipe Conejo Rodriguez Milan Oldřich Urban Marcela Santaella Javier Mauricio Gereda Aquiles Darghan Contreras Peter Wenzl |
| author_facet | Diego Felipe Conejo Rodriguez Milan Oldřich Urban Marcela Santaella Javier Mauricio Gereda Aquiles Darghan Contreras Peter Wenzl |
| author_sort | Diego Felipe Conejo Rodriguez |
| collection | DOAJ |
| description | IntroductionEvaluations of interspecific hybrids are limited, as classical genebank accession descriptors are semi-subjective, have qualitative traits and show complications when evaluating intermediate accessions. However, descriptors can be quantified using recognized phenomic traits. This digitalization can identify phenomic traits which correspond to the percentage of parental descriptors remaining expressed/visible/measurable in the particular interspecific hybrid. In this study, a line of P. vulgaris, P. acutifolius and P. parvifolius accessions and their crosses were sown in the mesh house according to CIAT seed regeneration procedures.MethodologyThree accessions and one derived breeding line originating from their interspecific crosses were characterized and classified by selected phenomic descriptors using multivariate and machine learning techniques. The phenomic proportions of the interspecific hybrid (line INB 47) with respect to its three parent accessions were determined using a random forest and a respective confusion matrix.ResultsThe seed and pod morphometric traits, physiological behavior and yield performance were evaluated. In the classification of the accession, the phenomic descriptors with highest prediction force were Fm’, Fo’, Fs’, LTD, Chl, seed area, seed height, seed Major, seed MinFeret, seed Minor, pod AR, pod Feret, pod round, pod solidity, pod area, pod major, pod seed weight and pod weight. Physiological traits measured in the interspecific hybrid present 2.2% similarity with the P. acutifolius and 1% with the P. parvifolius accessions. In addition, in seed morphometric characteristics, the hybrid showed 4.5% similarity with the P. acutifolius accession.ConclusionsHere we were able to determine the phenomic proportions of individual parents in their interspecific hybrid accession. After some careful generalization the methodology can be used to: i) verify trait-of-interest transfer from P. acutifolius and P. parvifolius accessions into their hybrids; ii) confirm selected traits as “phenomic markers” which would allow conserving desired physiological traits of exotic parental accessions, without losing key seed characteristics from elite common bean accessions; and iii) propose a quantitative tool that helps genebank curators and breeders to make better-informed decisions based on quantitative analysis. |
| first_indexed | 2024-04-11T13:32:49Z |
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| id | doaj.art-0956833b4bb94510905eeca81423dd18 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T13:32:49Z |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-0956833b4bb94510905eeca81423dd182022-12-22T04:21:43ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-12-011310.3389/fpls.2022.10086661008666Using phenomics to identify and integrate traits of interest for better-performing common beans: A validation study on an interspecific hybrid and its Acutifolii parentsDiego Felipe Conejo Rodriguez0Milan Oldřich Urban1Marcela Santaella2Javier Mauricio Gereda3Aquiles Darghan Contreras4Peter Wenzl5Genetic Resources Program, International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira, Valle del Cauca, ColombiaBean Physiology and Breeding Program, International Center for Tropical Agriculture, Recta Cali-Palmira, Valle del Cauca, ColombiaGenetic Resources Program, International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira, Valle del Cauca, ColombiaGenetic Resources Program, International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira, Valle del Cauca, ColombiaDepartment of Agronomy, Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Bogotá, ColombiaGenetic Resources Program, International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira, Valle del Cauca, ColombiaIntroductionEvaluations of interspecific hybrids are limited, as classical genebank accession descriptors are semi-subjective, have qualitative traits and show complications when evaluating intermediate accessions. However, descriptors can be quantified using recognized phenomic traits. This digitalization can identify phenomic traits which correspond to the percentage of parental descriptors remaining expressed/visible/measurable in the particular interspecific hybrid. In this study, a line of P. vulgaris, P. acutifolius and P. parvifolius accessions and their crosses were sown in the mesh house according to CIAT seed regeneration procedures.MethodologyThree accessions and one derived breeding line originating from their interspecific crosses were characterized and classified by selected phenomic descriptors using multivariate and machine learning techniques. The phenomic proportions of the interspecific hybrid (line INB 47) with respect to its three parent accessions were determined using a random forest and a respective confusion matrix.ResultsThe seed and pod morphometric traits, physiological behavior and yield performance were evaluated. In the classification of the accession, the phenomic descriptors with highest prediction force were Fm’, Fo’, Fs’, LTD, Chl, seed area, seed height, seed Major, seed MinFeret, seed Minor, pod AR, pod Feret, pod round, pod solidity, pod area, pod major, pod seed weight and pod weight. Physiological traits measured in the interspecific hybrid present 2.2% similarity with the P. acutifolius and 1% with the P. parvifolius accessions. In addition, in seed morphometric characteristics, the hybrid showed 4.5% similarity with the P. acutifolius accession.ConclusionsHere we were able to determine the phenomic proportions of individual parents in their interspecific hybrid accession. After some careful generalization the methodology can be used to: i) verify trait-of-interest transfer from P. acutifolius and P. parvifolius accessions into their hybrids; ii) confirm selected traits as “phenomic markers” which would allow conserving desired physiological traits of exotic parental accessions, without losing key seed characteristics from elite common bean accessions; and iii) propose a quantitative tool that helps genebank curators and breeders to make better-informed decisions based on quantitative analysis.https://www.frontiersin.org/articles/10.3389/fpls.2022.1008666/fullphenomic descriptorsphenomic proportionsinterspecific hybridimage analysismachine learning |
| spellingShingle | Diego Felipe Conejo Rodriguez Milan Oldřich Urban Marcela Santaella Javier Mauricio Gereda Aquiles Darghan Contreras Peter Wenzl Using phenomics to identify and integrate traits of interest for better-performing common beans: A validation study on an interspecific hybrid and its Acutifolii parents Frontiers in Plant Science phenomic descriptors phenomic proportions interspecific hybrid image analysis machine learning |
| title | Using phenomics to identify and integrate traits of interest for better-performing common beans: A validation study on an interspecific hybrid and its Acutifolii parents |
| title_full | Using phenomics to identify and integrate traits of interest for better-performing common beans: A validation study on an interspecific hybrid and its Acutifolii parents |
| title_fullStr | Using phenomics to identify and integrate traits of interest for better-performing common beans: A validation study on an interspecific hybrid and its Acutifolii parents |
| title_full_unstemmed | Using phenomics to identify and integrate traits of interest for better-performing common beans: A validation study on an interspecific hybrid and its Acutifolii parents |
| title_short | Using phenomics to identify and integrate traits of interest for better-performing common beans: A validation study on an interspecific hybrid and its Acutifolii parents |
| title_sort | using phenomics to identify and integrate traits of interest for better performing common beans a validation study on an interspecific hybrid and its acutifolii parents |
| topic | phenomic descriptors phenomic proportions interspecific hybrid image analysis machine learning |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1008666/full |
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