Home > IV Asian Horticultural Congress – AHC2023 > MARCO: a computer software for parentage inference using molecular markers

Articles

MARCO: a computer software for parentage inference using molecular markers

Article number

1404_83

Pages

613 – 618

Language

English

Abstract

Knowledge of parentage in agriculturally important conventional cultivars and genetic resources provides valuable information in breeding programs.
It is also important to verify an accurate parent-offspring relationship of a new cultivar with validated molecular markers for cultivar identification to protect the breeder’s rights.
We have developed the MARCO computer program for parentage analysis using multi-locus genotypes with co-dominant markers such as CAPS, SNPs, and SSR. MARCO does not incorporate probabilistic algorithms because the analysis target focuses on commercial cultivars, their ancestral varieties, and species rather than wild populations.
MARCO allows flexible estimation without probabilistic assumptions: parent to child, one parent and child to another parent, and both parents to a child.
In addition, each measure can allow for an arbitrary number of parent-child mismatches, exclude arbitrary markers, and perform estimations that include self-propagation.
These functions can be used, conversely, to validate DNA markers for cultivar identification with the genotype data set of confirmed parentage.
The program is designed to be user-friendly, with a graphical user interface and the ability to input and output in Excel.
As actual use examples, MARCO was applied to validate DNA markers for citrus cultivar identification.
Parentage analysis, in which stable and reproducible CAPS markers validated by MARCO were used, revealed that satsuma mandarin (Citrus unshiu) is derived from the natural cross between kishu mandarin (C. kinokuni) and kunenbo mandarin (C. nobilis). We also confirmed the parentage of major citrus commercial cultivars is correct, such as ‘Kiyomi’ (satsuma mandarin × sweet orange (C. sinensis)), ‘Harumi’ (‘Kiyomi’ × ponkan (C. reticulata)), and ‘Shiranuhi’ (‘Kiyomi’ × ponkan), which were established in Japanese breeding programs.
MARCO can be used under the license from NARO (National Agricultural Research Organization of Japan).

Publication

IV Asian Horticultural Congress – AHC2023

Authors

H. Fujii, F. Hosaka, T. Endo, T. Shimada, S. Terakami, T. Yamamoto

Keywords

CAPS, citrus, cultivar, genotype, SNPs, SSR

Full text

https://doi.org/10.17660/ActaHortic.2024.1404.83

Groups involved

Online Articles (205)

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181. Effects of rain-protected culture in a plastic greenhouse using the whole harvest cultivation method for one-year-old asparagus plants

S. Yamashita | K. Seimiya | K. Yamafuji | T. Taguchi | S. Motoki

182. Estimation of the light extinction coefficients of lateral asparagus ferns using a numerical method

T. Kuroyanagi | H. Yoshikoshi | M. Hikawa-Endo

183. Glycine betaine material affects the growth and yield of asparagus in the long-term harvest production system in a semi-forcing culture

F. Satake | K. Okada | Y. Yoshida | W. Sakata | S. Motoki

184. Mounding increases the rate of thick spears of asparagus

K. Suzuki | Y. Ayabe | A. Kato | S. Motoki

185. Investigation of nutrient solution management in hydroponics using organic fertilizer

T. Endoh | M. Takagaki | P. Suwitchyanon | C. Chaturong

186. Effect of different cultivation methods and environments on the growth and yield of Shimonita-Negi

M. Okabe | K. Obokata | T. Hirose | Y. Hashida

187. Predicting corn salad (Valerianella spp.) weight in a plant factory with artificial lighting (PFAL) using K-Nearest Neighbors algorithm (KNN)

S. Dhammayorddee | C. Chanseetis | A. Kato | M. Takagaki | N. Lookin

188. The effect of water and fertilizer types on growth and yield of supan-supan (Neptunia oleracea) cultivated on flooded Ultisol media

H. Susanti | J. Purnomo | O.A. Kumadawara

189. Effect of low sunlight and high temperature during flower bud differentiation on the cut flower quality of carnation ‘Cherry Tessino’

S. Kamachi | R. Sakai | S. Nagashima | S. Mori

190. Deficit irrigation and fertilizer rates affecting growth, flower quality and physiological changes in tuberous begonia grown in plant factory

C. Inkham | K. Panjama | S. Ruamrungsri

191. Growth and flowering characteristics of Calendula under different light spectra in a controlled environment

M. Munyanont | N. Lu | T. Joilek | D.F. Rachma | M. Takagaki

192. Selection of optimal marigold (Tagetes patula) cultivar as an edible flower in a plant factory

N.Y. Kwak | B.H. Sung | K.P.S. Kumaratenna | Y.Y. Cho

193. Promoting flower yields, photosynthetic pigments and some secondary metabolite in Marguerite daisy (Chrysanthemum frutescens L.) cut flower under the smart farming system by pinching technique

Y. Luekhampa | C. Seelatlao | W. Chareontham | J. Sanitchon | P. Hongpakdee

194. Nutrient deficiencies affect growth and development of vinca

S. Ruamrungsri | C. Inkham | K. Panjama

195. Relationship between Asian ginseng decline and soil chemical property

Md.A.A. Mahmud | Y. Matsubara | T. Ikezawa

196. Influence of different flower vases on the impression of cut flowers

Y. Mitarai

197. Effects of different LED light spectrum on growth and cannabinoid contents of Cannabis sativa L. hybrid ‘KKU’ cultivars under an indoor pot cultivation

P. Nounbunma | P. Hongpakdee | J. Paluka | C. Lapjit

198. Effects of cultivation environmental factors on the growth of the edible cactus (Nopalea cochenillifera) grown under hydroponic conditions

S. Tsuchimoto | K. Okada | K. Kondo | T. Horibe

199. Calcium and magnesium biofortification of the edible cactus Nopalea cochenillifera grown under hydroponic conditions

E. Nishimura | K. Hayashi | T. Horibe

200. Effect of selling area, period, and type on the price of okra (Abelmoschus esculentus L.) in Japan

L. Sato | N. Miyamoto | S. Motoki

201. Comparative analysis of asparagus marketing practices in Europe, North America, and Asia during summer and autumn

S. Yamashita | S. Motoki

202. Edible alleys in the discourse of urban horticulture: a case study on densely built urban renewal districts in Chiayi, Taiwan

T.I. Lee

203. Application of calcium chloride on yield and quality of Capsicum annuum L.

N. Montri | S. Sengseng | R. Deewatthanawong | K. Bunya-atichart

204. Development of a growth state estimation system using a moving camera in strawberry cultivation

S. Matsuo | H. Umeda

205. The impact of adding nanoparticles to the media to speed up the in vitro multiplication stage of banana explants

P. Nugrahani | I.R. Moeljani