Reference-Guided De Novo Genome Assembly to Dissect a QTL Region for Submergence Tolerance Derived from Ciherang-Sub1.

Yuya Liang,Nithya K Subramanian,Charles D Johnson,Shichen Wang,Julia Bailey-Serres,Chersty L Harper,Rodante E Tabien,Endang M Septiningsih

doi:10.3390/plants10122740

Yuya Liang, Nithya K Subramanian + Show 6 more

Open Access

https://doi.org/10.3390/plants10122740

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Abstract

Global climate change has increased the number of severe flooding events that affect agriculture, including rice production in the U.S. and internationally. Heavy rainfall can cause rice plants to be completely submerged, which can significantly affect grain yield or completely destroy the plants. Recently, a major effect submergence tolerance QTL during the vegetative stage, qSub8.1, which originated from Ciherang-Sub1, was identified in a mapping population derived from a cross between Ciherang-Sub1 and IR10F365. Ciherang-Sub1 was, in turn, derived from a cross between Ciherang and IR64-Sub1. Here, we characterize the qSub8.1 region by analyzing the sequence information of Ciherang-Sub1 and its two parents (Ciherang and IR64-Sub1) and compare the whole genome profile of these varieties with the Nipponbare and Minghui 63 (MH63) reference genomes. The three rice varieties were sequenced with 150 bp pair-end whole-genome shotgun sequencing (Illumina HiSeq4000), followed by performing the Trimmomatic-SOAPdenovo2-MUMmer3 pipeline for genome assembly, resulting in approximate genome sizes of 354.4, 343.7, and 344.7 Mb, with N50 values of 25.1, 25.4, and 26.1 kb, respectively. The results showed that the Ciherang-Sub1 genome is composed of 59–63% Ciherang, 22–24% of IR64-Sub1, and 15–17% of unknown sources. The genome profile revealed a more detailed genomic composition than previous marker-assisted breeding and showed that the qSub8.1 region is mostly from Ciherang, with some introgressed segments from IR64-Sub1 and currently unknown source(s).

Highlights

Rice (Oryza sativa L.) is a staple food that feeds nearly half of the world’s population [1].Complete submergence of rice reduces the availability of carbon dioxide and oxygen, reducing photosynthesis and limiting the aerobic metabolism, which together can dramatically reduce crop productivity [2]
The results showed that the Ciherang-Submergence 1 (Sub1) genome is composed of 59–63% Ciherang, 22–24% of IR64-Sub1, and 15–17% of unknown sources
The results showed that Ciherang-Sub1, Ciherang, and IR64-Sub1 had genome sizes of 345.4, 343.7, and 344.7 Mb, which correspond to 92.2–92.6% coverage on the Nipponbare reference genome 4(Toafb1l2e 1)

Summary

Introduction

Complete submergence of rice reduces the availability of carbon dioxide and oxygen, reducing photosynthesis and limiting the aerobic metabolism, which together can dramatically reduce crop productivity [2]. Extreme weather events have increased the frequency of severe flooding, which significantly affects agriculture, including rice production in the U.S and globally. The key gene of this locus is Sub1A-1, encoding an ethylene-responsive factor (ERF) in subgroup VII, which is activated by ethylene that accumulates in submerged tissues [13]. The linked Sub1B and Sub1C genes encode the most related ERFs in the genome, indicating this locus arose through tandem duplication [14] prior to domestication [15]

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