NDLI: Intuitive Visual Impressions (Cogs) for Identifying Clusters of Diversity within Potato Species

Content Provider	Springer Nature Link
Author	Bamberg, John Rio, Alfonso Navarre, Duroy A.
Copyright Year	2016
Abstract	One of the basic research activities of genebanks is to partition stocks into groups that facilitate the efficient preservation and evaluation of the full range of useful phenotype diversity. We sought to test the usefulness of making intraspecific groups by replicated rapid visual intuitive impressions of coded plants by multiple uncoached observers. We invented the term “cog” (shorthand for cognate = “born together”) to indicate assumed genetic relatedness of cog members. All of the 16 populations of the wild potato species Solanum okadae in the genebank were thus examined in four separate grow-outs by up to seven genebank staff members, a total of 26 times. They were instructed to place them into two cogs defined only as big and not-big. Four populations were placed in the big cog for 70–90 % of observations, while all remaining populations but one were placed in the big cog for less than 5 % of observations. All populations were then assessed for DNA markers and various empirical traits. AFLP and SNP markers clearly distinguished the two cogs. The big cog populations were also distinguished from the others by virtue of having less foliar late blight resistance, more leaf hairiness, and lower tuber tomatine content. SNP similarity suggests one population of reputed Bolivian origin is really a mislabeled duplicate of another from Argentina. If so, the two cogs also perfectly align with country of natural origin, with big originating exclusively from Bolivia. Using S. okadae as a model, we demonstrated that rapid, simple, and inexpensive visual intuitive cogs reliably predict significant genetic and phenotypic differences. We propose testing the cog technique on other species and applying it as a new potato germplasm descriptor.Una de las actividades básicas de investigación de los bancos de germoplasma, es dividir los materiales en grupos que faciliten la preservación eficiente y la evaluación de la completa amplitud de diversidad de fenotipos útiles. Buscamos probar la utilidad de hacer grupos intra-específicos mediante impresiones rápidas, visuales, intuitivas, de plantas codificadas por múltiples observadores sin influencias. Inventamos el término “cog” (abreviación para cognate = “nacidos juntos”) para indicar relación genética asumida de números cog. Todas las 16 poblaciones de las especies silvestres de papa Solanum okadae en el banco de germoplasma fueron examinadas así en cuatro crecimientos separados por hasta 7 miembros del personal del banco de germoplasma, un total de 26 veces. Se les instruyó para ubicarlas en dos cogs definidos, solo grandes y no grandes. Se ubicaron cuatro poblaciones en el cog grande por 70–90 % de observaciones, mientras que todas las poblaciones restantes, excepto una, se ubicaron en el cog grande para menos del 5 % de las observaciones. Entonces todas las poblaciones fueron analizadas por marcadores de ADN y varios caracteres empíricos. Los marcadores AFLP y SNP distinguieron claramente los dos cogs. Las poblaciones del cog grande se distinguieron también de las otras por la característica de tener menos resistencia foliar al tizón tardío, más vellosidad en las hojas, y más bajo contenido de tomatina en el tubérculo. La similitud en los SNP sugiere que una población de origen asumido boliviano es realmente un duplicado etiquetado erróneamente de otro de Argentina. Si asi es, los dos cogs también se alinean perfectamente con el país de origen natural, con grande originándose exclusivamente de Bolivia. Usando S. okadae como modelo, demostramos que cogs visuales intuitivos rápidos, simples y baratos predicen confiablemente diferencias significativas genéticas y fenotípicas. Proponemos que se pruebe la técnica cog en otras especies y que se aplique como un nuevo descriptor de germoplasma de papa.
Starting Page	350
Ending Page	359
Page Count	10
File Format	PDF
ISSN	1099209X
Journal	American Potato Journal
Volume Number	93
Issue Number	4
e-ISSN	18749380
Language	English
Publisher	Springer US
Publisher Date	2016-04-29
Publisher Institution	Potato Association of America
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Intuitive clusters Classification Cog Germplasm Predictivity Plant Sciences Agriculture Plant Genetics & Genomics Plant Breeding/Biotechnology Plant Pathology
Content Type	Text
Resource Type	Article
Subject	Plant Science Agronomy and Crop Science

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
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8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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