**Development of Chromosome Segment Substitution Lines (CSSLs) Derived from Guangxi Wild Rice (***Oryza rufipogon* **Gri**ff**.) under Rice (***Oryza sativa* **L.) Background and the Identification of QTLs for Plant Architecture, Agronomic Traits and Cold Tolerance**

### **Ruizhi Yuan** †**, Neng Zhao** †**, Babar Usman** †**, Liang Luo, Shanyue Liao, Yufen Qin, Gul Nawaz and Rongbai Li \***

State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; 1717303012@st.gxu.edu.cn (R.Y.); nengzhao@st.gxu.edu.cn (N.Z.); babarusman119@gmail.com (B.U.); 1717303001@st.gxu.edu.cn (L.L.); 1817303014@st.gxu.edu.cn (S.L.); qyf@st.gxu.edu.cn (Y.Q.); gulnawazmalik@yahoo.com (G.N.)

**\*** Correspondence: lirongbai@gxu.edu.cn or lirongbai@126.com; Tel.: +86-136-0009-4135

† These authors contributed equally to this work.

Received: 12 July 2020; Accepted: 21 August 2020; Published: 22 August 2020

**Abstract:** Common wild rice contains valuable resources of novel alleles for rice improvement. It is well known that genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segmen<sup>t</sup> substitution lines (CSSLs) ais a powerful tool for fine mapping of quantitative traits, new gene discovery and marker-assisted breeding. In this study, 132 CSSLs were developed from a cultivated rice (*Oryza sativa*) cultivar (93-11) and common wild rice (*Oryza rufipogon* Griff. DP30) by selfing-crossing, backcrossing and marker-assisted selection (MAS). Based on the high-throughput sequencing of the 93-11 and DP30, 285 pairs of Insertion-deletions (InDel) markers were selected with an average distance of 1.23 Mb. The length of this DP30-CSSLs library was 536.4 cM. The coverage rate of substitution lines cumulatively overlapping the whole genome of DP30 was about 91.55%. DP30-CSSLs were used to analyze the variation for 17 traits leading to the detection of 36 quantitative trait loci (QTLs) with significant phenotypic effects. A cold-tolerant line (RZ) was selected to construct a secondary mapping F2 population, which revealed that *qCT2.1* is in the 1.7 Mb region of chromosome 2. These CSSLs may, therefore, provide powerful tools for genome wide large-scale gene discovery in wild rice. This research will also facilitate fine mapping and cloning of QTLs and genome-wide study of wild rice. Moreover, these CSSLs will provide a foundation for rice variety improvement.

**Keywords:** rice; chromosome segmen<sup>t</sup> substitution lines (CSSLs); quantitative trait locus (QTL); marker-assisted selection (MAS); cold tolerance (CT)
