Plants 2022, 11, 788. https://doi.org/10.3390/plants11060788 www.mdpi.com/journal/plants Article Novel QTL Associated with Aerenchyma-Mediated Radial Oxygen Loss (ROL) in Rice (Oryza sativa L.) under Iron (II) Sulfide Dang Van Duyen 1,† , Youngho Kwon 2,† , Nkulu Rolly Kabange 2,†, *, Ji-Yoon Lee 2 , So-Myeong Lee 2 , Ju-Won Kang 2 , Hyeonjin Park 2 , Jin-Kyung Cha 2 , Jun-Hyeon Cho 2 , Dongjin Shin 2 and Jong-Hee Lee 2, * 1 Molecular Biology Department, Agricultural Genetic Institute, Hanoi 11917, Vietnam; dangvanduyen79@gmail.com 2 Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Korea; kwon6344@korea.kr (Y.K.); minitia@korea.kr (J.-Y.L.); olivetti90@korea.kr (S.-M.L.); kangjw81@korea.kr (J.-W.K.); tinapark@korea.kr (H.P.); jknzz5@korea.kr (J.-K.C.); hy4779@korea.kr (J-H.C.); jacob1223@korea.kr (D.S.) * Correspondence: rollykabange@korea.kr (N.R.K.); ccriljh@korea.kr (J.-H.L.); Tel.: +8210-5413-4881 (N.R.K.); +82–53–350–1169 (J.-H.L.); Fax: +82–55–352–3059 (J.-H.L.) † These authors contributed equally to this work. Abstract: In rice, high radial oxygen loss (ROL) has been associated with the reduction in the activity of methanogens, therefore reducing the formation of methane (CH4) due to the abundance in appli- cation of nitrogen (N)-rich fertilizers. In this study, we evaluated the root growth behavior and ROL rate of a doubled haploid (DH) population (n = 117) and parental lines 93-11 (P1, indica) and Mi- lyang352 (P2, japonica) in response to iron (II) sulfide (FeS). In addition, we performed a linkage mapping and quantitative trait locus (QTL) analysis on the same population for the target traits. The results of the phenotypic evaluation revealed that parental lines had distinctive root growth and ROL patterns, with 93-11 (indica) and Milyang352 (japonica) showing low and high ROL rates, respectively. This was also reflected in their derived population, indicating that 93.2% of the DH lines exhibited a high ROL rate and about 6.8% had a low ROL pattern. Furthermore, the QTL and linkage map analysis detected two QTLs associated with the control of ROL and root area on chro- mosomes 2 (qROL-2-1, 127 cM, logarithm of the odds (LOD) 3.04, phenotypic variation explained (PVE) 11.61%) and 8 (qRA-8-1, 97 cM, LOD 4.394, PVE 15.95%), respectively. The positive additive effect (2.532) of qROL-2-1 indicates that the allele from 93-11 contributed to the observed phenotypic variation for ROL. The breakthrough is that the qROL-2-1 harbors genes proposed to be involved in stress signaling, defense response mechanisms, and transcriptional regulation, among others. The qPCR results revealed that the majority of genes harbored by the qROL-2-1 recorded a higher tran- script accumulation level in Milyang352 over time compared to 93-11. Another set of genes exhib- ited a high transcript abundance in P1 compared to P2, while a few were differentially regulated between both parents. Therefore, OsTCP7 and OsMYB21, OsARF8 genes encoding transcription fac- tors (TFs), coupled with OsTRX, OsWBC8, and OsLRR2 are suggested to play important roles in the positive regulation of ROL in rice. However, the recorded differential expression of OsDEF7 and OsEXPA, and the decrease in OsNIP2, Oscb5, and OsPLIM2a TF expression between parental lines proposes them as being involved in the control of oxygen flux level in rice roots. Keywords: radial oxygen loss; aerenchyma; quantitative trait locus; greenhouse gas; rice 1. Introduction Oryza sativa L. remains the most cultivated species of rice across the world and com- prises the indica and japonica subspecies [1]. The two rice subspecies are reported to have Citation: Van Duyen, D.; Kwon, Y.; Kabange, N.R.; Lee, J.-Y.; Lee, S.-M.; Kang, J.-W.; Park, H.; Cha, J.-K.; Cho, J.-H.; Shin, D.; et al. Novel QTL Associated with Aerenchyma- Mediated Radial Oxygen Loss (ROL) in Rice (Oryza sativa L.) under Iron (II) Sulfide. Plants 2022, 11, 788. https://doi.org/10.3390/ plants11060788 Academic Editor: Srinivasan Ramachandran Received: 20 December 2021 Accepted: 15 March 2022 Published: 16 March 2022 Publisher’s Note: MDPI stays neu- tral with regard to jurisdictional claims in published maps and institu- tional affiliations. Copyright: © 2022 by the authors. Li- censee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and con- ditions of the Creative Commons At- tribution (CC BY) license (https://cre- ativecommons.org/licenses/by/4.0/).