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QTL Mapping and Expression Analysis of Candidate Genes for Salt and Drought Tolerance in Corchorus capsularis Seedlings

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Abstract

Jute is an essential fibrous crop worldwide. However, salt- and drought-induced stresses affect its production. The complex inheritance for such traits makes Quantitative Trait Loci (QTL) detection cumbersome when using the approach to understand and improve the plant’s tolerance to these stresses. There is a need to identify the underlying mechanistic events under these stress conditions at the seedling stage. Therefore, this study uses genetic and transcriptomic approaches to identify the markers, QTL and candidate genes related to salt and drought tolerance in jute. We also analyzed some phenotypes, including dry root weight (DRW), dry shoot weight (DSW), root fresh weight (RFW), root length (RL), relative water content (RWC), shoot fresh weight (SFW) and Shoot length (SL). One hundred (100) recombinant inbred lines (RILs) of the white Jute and the parents were evaluated under control, salt and drought conditions. Analysis of variance indicates significant differences (p < 0.01) among the RILs, and the estimates of broad-sense heritability of the RILs ranges from 50.0 to 98.5%. Two QTL for RL and SL under drought (qRLD-1–1 and qSLD-1–1, respectively) were found in the same position and associated with the flanking markers Marker5166 and Marker7753. Moreover, qRWCS-1–1 for the relative water content under salt treatment had the highest Phenotypic Variation Explained (PVE, 24.63%) with the flanking markers Marker19007 and Marker28120. Our results suggest that these genes regulate the two stresses at the seedling stage in Corchorus capsularis and function in different pathways. However, further study is needed to validate this. Higher additive effects were observed in sodium chloride (NaCl)-induced stress which suggest that salt stress selection would be more effective and useful at the seedling stage. The relative expression analysis of the candidate genes and the phenotypes of the samples reveal that CCACVL1_12635 and CCACVL1_15402, and CCACVL1_23216 genes are the salt and drought tolerance candidate genes, respectively, and function in the cystatin and potassium ion transporter 1 (KT1) pathways.

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Abbreviations

QTL:

Quantitative Trait Loci

SLAF:

Specific Locus Amplified Fragment

PVE:

Phenotypic Variation Explained

RFLP:

Restriction Fragment Length Polymorphisms

MAS:

Marker Assistant Selection

PEG:

Polyethylene Glycol

RIL:

Recombinant Inbred Lines

DRW:

Dry Root Weight

DSW:

Dry Shoot Weight

RFW:

Root Fresh Weight

RWC:

Relative Water Content

SFW:

Shoot Fresh Weight

RL:

Root Length

SL:

Shoot Length

ANOVA:

Analysis of Variance

LOD:

Logarithm of Odds

LG:

Linkage Group

ROS:

Reactive Oxygen Species

q :

QTL

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Acknowledgements

National Natural Science Foundation of China supported this work (31771369) and China Agriculture Research System (CARS-19E06).

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Authors and Affiliations

  1. Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding By, Design/College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Aminu Kurawa Ibrahim, Yi Xu, Sylvain Niyitanga, Muhammad Zohaib Afzal, Lilan Zhang, Liemei Zhang, Jianmin Qi & Liwu Zhang

  2. Experiment Station of Jute and Kenaf in Southeast China of Ministry of Agriculture and Rural Affairs/Public Platform for Germplasm Resources of Southern Bast Fiber Crops of Fujian, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Aminu Kurawa Ibrahim, Yi Xu, Sylvain Niyitanga, Muhammad Zohaib Afzal, Lilan Zhang, Liemei Zhang & Jianmin Qi

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  1. Aminu Kurawa Ibrahim
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  2. Yi Xu
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  3. Sylvain Niyitanga
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  4. Muhammad Zohaib Afzal
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  5. Lilan Zhang
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  6. Liemei Zhang
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  8. Liwu Zhang
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Contributions

Aminu Kurawa Ibrahim; methodology, writing original draft, formal analysis, data curation, editing, Yi Xu; resources and data curation, Sylvain Niyitanga; editing, Muhammad Zohaib Afzal; editing, Lilan Zhang; editing, Liemei Zhang; editing, Jianmin Qi; visualization and supervision, Liwu Zhang; software, validation, supervision, project administrator as well as funding acquisition.

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Correspondence to Liwu Zhang.

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Supplementary Information

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12042_2021_9292_MOESM1_ESM.docx

Supplementary file1 Supplementary Figure 1: Genetic map of white Jute at seedling stage with QTL in LGs 1 to 11 based on F8 RILs population. The number of linkage groups are indicated at the top. While markers and the genetic distances are presented at the right and left of the map, respectively. (DOCX 3588 KB)

12042_2021_9292_MOESM2_ESM.docx

Supplementary file2 Supplementary Figure 2: Additive and logarithm of the odds in all the chromosomes on SL (shoot length), RL (root length), SPDV (SPAD value) and RWC (relative water content) under salt treatment condition (S). (a): Shoot length under salt treatment condition (SLS). (b): Root length under salt treatment condition (RLS). (c): Chlorophyll content (SPDVS). (d): Relative water content (RWCS). (DOCX 1300 KB)

Supplementary file3 Supplementary Table 1: Primer sequences used for the candidate and reference genes. (DOCX 13 KB)

Supplementary file4 (RAR 2624 KB)

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Ibrahim, A.K., Xu, Y., Niyitanga, S. et al. QTL Mapping and Expression Analysis of Candidate Genes for Salt and Drought Tolerance in Corchorus capsularis Seedlings. Tropical Plant Biol. 14, 345–359 (2021). https://doi.org/10.1007/s12042-021-09292-5

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