Copy Number Quantification for the Soybean Cyst Nematode Resistance Locus rhg1 in the Soybean Varieties of Taiwan

Cheng-Chun Huang,Hao-Xun Chang,Chen-Hsiang Lin,Kuo-Lung Chou,Jiue-In Yang

doi:10.3390/agronomy11071346

Cheng-Chun Huang, Hao-Xun Chang + Show 3 more

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https://doi.org/10.3390/agronomy11071346

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Journal: Agronomy	Publication Date: Jun 30, 2021
Citations: 3	License type: CC BY 4.0

Affiliation: National Taiwan University, Council of Agriculture

Abstract

Disease resistance is one of the most successful strategies in crop protection. For example, the implementation of PI 88788 type resistance, which contains high copy numbers of Resistance to Heterodera glycines 1 (rhg1) loci, into the commercial soybean varieties of the United States has significantly reduced the yield losses caused by soybean cyst nematode (SCN, H. glycines). Vegetable soybean, or edamame, has become a major exporting agricultural product in Taiwan with an annual revenue over $80 million USD since 2017. Several local varieties have been developed to fulfill the market needs such as the traits of flavor and sweetness. However, it remains unclear if the historical breeding programs ever incorporated rhg1 resistance into the varieties of Taiwan. This study applied the TaqMan qPCR method to measure the fluorescent signals specific to the rhg1 locus on the chromosome 18 of soybean, and the ratio of VIC and FAM signals were analyzed to predict the rhg1 copy number in the 21 soybean varieties of Taiwan. The results indicated the copy number and the single nucleotide polymorphisms of the 21 soybean varieties were identical to the susceptible soybean variety ‘Williams 82’. As importation of soybean will be continuously needed to fulfill the market and because SCN is absent in the soybean fields of Taiwan, lacking rhg1 resistance in the local soybean varieties may put the edamame industry at risk and early implementation of SCN resistance in the breeding program, alongside the application of quarantine regulations, will be the key to maintain the SCN-free status and to sustain the edamame industry in Taiwan.

Highlights

Soybean cyst nematode (SCN, Heterodera glycines) is the major yield-limiting biotic stress for soybean production worldwide [1]
The modified TaqMan method was applied to the 21 soybean varieties of Taiwan, and the Relative fluorescence units (RFU) of the 21 soybean varieties scattered closely to the W type locus, and none of the 99% confidence interval overlapped with “Peking” or plant introduction (PI) 88788 or PI 209332
The Gaussian, Poisson, and negative binomial models were selected based on the Akaike information criterion (AIC) and Bayesian information criterion (BIC) statistics, and the results indicated that Box–Cox-transformed Gaussian linear model was the best regression based on the lower AIC and BIC value (Table 2)

Summary

Introduction

Soybean cyst nematode (SCN, Heterodera glycines) is the major yield-limiting biotic stress for soybean production worldwide [1]. The earliest report of cyst nematodes in soybean was documented in Japan [2] as Heterodera schachtii Schmidt [3], and was not reclassified as Heterodera glycines Ichinohe until 1952 [4]. The obligate endoparasitic plant nematode has been globally distributed in the major soybean-producing countries including the US, Argentina, Brazil, and China [5]. SCN infects soybean roots, leading to the stunting and yellowing of the host. SCN infection often increases soybean susceptibility to fungal infection, which synergistically reduces the yield drastically. SCN caused annual yield losses of about 100 million bushels during 2006 to 2014 [6,7] and it is responsible for approximately over $1 billion loss per year in the United States

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