Development of a leafy Brassica rapa fixed line collection for genetic diversity and population structure analysis

Pang, Wenxing; Li, Xiaonan; Choi, Su Ryun; Dhandapani, Vignesh; Im, Subin; Park, Min Young; Jang, Chang Soon; Yang, Man-Sung; Ham, In Ki; Lee, Eun Mo; Kim, Wankyu; Lee, Soo-Seong; Bonnema, Guusje; Park, Suhyoung; Piao, Zhongyun; Lim, Yong Pyo

doi:10.1007/s11032-015-0221-9

Cited by 15 publications

(11 citation statements)

References 40 publications

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“…Previous studies have attempted to identify genetically discrete groups among B. rapa crops with molecular markers (Del Carpio et al., ,b; Guo, Chen, Li, & Cowling, ; McGrath & Quiros, ; Pang et al., ; Ren, McFerson, Li, Kresovich, & Lamboy, ; Takahashi, Yokoi, & Takahata, ; Takuno, Kawahara, & Ohnishi, ; Tanhuanpää, Erkkilä, Tenhola‐Roininen, Tanskanen, & Manninen, ; Zhao et al., , , ). Most analyses identify three ambiguous geographic groups present in Europe and Central Asia, South Asia and East Asia (Del Carpio et al., ,b; Guo et al., ; Pang et al., ) except a recent analysis that found no evidence for geographic structure among diverse B. rapa accessions (Tanhuanpää et al., ). In addition, previous genetic and empirical studies suggested two distinct hypotheses for the origin of Chinese cabbage: domesticated directly from pak choi (Song, Osborn, & Williams, ; Takuno et al., ; Zhao et al., ) or via genetic admixture of turnip and pak choi (Li, ; Ren et al., ).…”

Section: Introductionmentioning

confidence: 99%

Genomic inferences of domestication events are corroborated by written records in Brassica rapa

Ragsdale

et al. 2017

Molecular Ecology

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Demographic modelling is often used with population genomic data to infer the relationships and ages among populations. However, relatively few analyses are able to validate these inferences with independent data. Here, we leverage written records that describe distinct Brassica rapa crops to corroborate demographic models of domestication. Brassica rapa crops are renowned for their outstanding morphological diversity, but the relationships and order of domestication remain unclear. We generated genomewide SNPs from 126 accessions collected globally using high-throughput transcriptome data. Analyses of more than 31,000 SNPs across the B. rapa genome revealed evidence for five distinct genetic groups and supported a European-Central Asian origin of B. rapa crops. Our results supported the traditionally recognized South Asian and East Asian B. rapa groups with evidence that pak choi, Chinese cabbage and yellow sarson are likely monophyletic groups. In contrast, the oil-type B. rapa subsp. oleifera and brown sarson were polyphyletic. We also found no evidence to support the contention that rapini is the wild type or the earliest domesticated subspecies of B. rapa. Demographic analyses suggested that B. rapa was introduced to Asia 2,400-4,100 years ago, and that Chinese cabbage originated 1,200-2,100 years ago via admixture of pak choi and European-Central Asian B. rapa. We also inferred significantly different levels of founder effect among the B. rapa subspecies. Written records from antiquity that document these crops are consistent with these inferences. The concordance between our age estimates of domestication events with historical records provides unique support for our demographic inferences.

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Section: Introductionmentioning

confidence: 99%

Genomic inferences of domestication events are corroborated by written records in Brassica rapa

Ragsdale

et al. 2017

Molecular Ecology

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“…Despite the economic importance and historical records of B. rapa crops, our understanding of their relationships and origins is still not well resolved. Previous studies have attempted to identify genetically discrete groups among B. rapa crops with molecular markers (McGrath & Quiros 1992;Ren et al 1995;Zhao et al 2005Zhao et al , 2007Zhao et al , 2010Takuno et al 2006;Del Carpio et al 2011a;Guo et al 2014;Pang et al 2015;Takahashi et al 2015;Tanhuanpää et al 2016) . Most analyses identify three ambiguous geographic groups present in Europe and Central Asia, South Asia, and East Asia (Del Carpio et al 2011a;Guo et al 2014;Pang et al 2015) except a recent analysis that found no evidence for geographic structure among diverse B. rapa accessions (Tanhuanpää et al 2016) .…”

Section: Introductionmentioning

confidence: 99%

“…Previous studies have attempted to identify genetically discrete groups among B. rapa crops with molecular markers (McGrath & Quiros 1992;Ren et al 1995;Zhao et al 2005Zhao et al , 2007Zhao et al , 2010Takuno et al 2006;Del Carpio et al 2011a;Guo et al 2014;Pang et al 2015;Takahashi et al 2015;Tanhuanpää et al 2016) . Most analyses identify three ambiguous geographic groups present in Europe and Central Asia, South Asia, and East Asia (Del Carpio et al 2011a;Guo et al 2014;Pang et al 2015) except a recent analysis that found no evidence for geographic structure among diverse B. rapa accessions (Tanhuanpää et al 2016) . In addition, previous genetic and empirical studies suggested two distinct hypotheses for the origin of Chinese cabbage: domesticated directly from pak choi (Song et al 1990;Zhao et al 2005;Takuno et al 2006) or via genetic admixture of turnip and pak choi (Li 1981;Ren et al 1995) .…”

Section: Introductionmentioning

confidence: 99%

Genomic inferences of domestication events are corroborated by written records inBrassica rapa

Ragsdale

et al. 2017

Preprint

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Demographic modeling is often used with population genomic data to infer the relationships and ages among populations. However, relatively few analyses are able to validate these inferences with independent data. Here, we leverage written records that describe distinct Brassica rapa crops to corroborate demographic models of domestication. Brassica rapa crops are renowned for their outstanding morphological diversity, but the relationships and order of domestication remains unclear. We generated genome-wide SNPs from 126 accessions collected globally using high-throughput transcriptome data. Analyses of more than 31,000 SNPs across the B. rapa genome revealed evidence for five distinct genetic groups and supported a European-Central Asian origin of B. rapa crops. Our results supported the traditionally recognized South Asian and East Asian B. rapa groups with evidence that pak choi, Chinese cabbage, and yellow sarson are likely monophyletic groups. In contrast, the oil-type B. rapa subsp. oleifera and brown sarson were polyphyletic. We also found no evidence to support the contention that rapini is the wild type or the earliest domesticated subspecies of B. rapa .

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“…We used 156 lines of the B. rapa core collection to produce three datasets for the development of classification models based on the morphology of Chinese cabbage (Pang et al, 2015 ). The individual lines in the core collection are classified as Chinese accessions, early introduced accessions, Korean breeding accessions, or non-pekinensis accessions depending on their geographic origin ( Figure 1 ).…”

Section: Methodsmentioning

confidence: 99%

Deep Learning Algorithms Correctly Classify Brassica rapa Varieties Using Digital Images

Jung

Song²,

Hong

et al. 2021

Front. Plant Sci.

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Efficient and accurate methods of analysis are needed for the huge amount of biological data that have accumulated in various research fields, including genomics, phenomics, and genetics. Artificial intelligence (AI)-based analysis is one promising method to manipulate biological data. To this end, various algorithms have been developed and applied in fields such as disease diagnosis, species classification, and object prediction. In the field of phenomics, classification of accessions and variants is important for basic science and industrial applications. To construct AI-based classification models, three types of phenotypic image data were generated from 156 Brassica rapa core collections, and classification analyses were carried out using four different convolutional neural network architectures. The results of lateral view data showed higher accuracy compared with top view data. Furthermore, the relatively low accuracy of ResNet50 architecture suggested that definition and estimation of similarity index of phenotypic data were required before the selection of deep learning architectures.

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Development of a leafy Brassica rapa fixed line collection for genetic diversity and population structure analysis

Cited by 15 publications

References 40 publications

Genomic inferences of domestication events are corroborated by written records in Brassica rapa

Genomic inferences of domestication events are corroborated by written records in Brassica rapa

Genomic inferences of domestication events are corroborated by written records inBrassica rapa

Deep Learning Algorithms Correctly Classify Brassica rapa Varieties Using Digital Images

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