Salt Tolerance Improvement in Rice through Efficient SNP Marker-Assisted Selection Coupled with Speed-Breeding

• Published in: International journal of molecular sciences Vol. 20; no. 10; p. 2585
• Main Authors: Rana, Md Masud, Takamatsu, Takeshi, Baslam, Marouane, Kaneko, Kentaro, Itoh, Kimiko, Harada, Naoki, Sugiyama, Toshie, Ohnishi, Takayuki, Kinoshita, Tetsu, Takagi, Hiroki, Mitsui, Toshiaki
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 26-05-2019; MDPI
• Subjects: Agricultural production; Agronomy; Barley; Brassica napus; Chickpeas; Cicer arietinum; Cultivars; Fertilization; Genes; Genomes; Genomics; Genotype & phenotype; Hordeum vulgare; hst1; HST1 gene; Marker-assisted selection; Markers; Mutants; Na+ accumulation; Pisum sativum; Plant breeding; rapid generation advance; Rice; Salinity; Salinity tolerance; salt tolerant; Self-fertilization; Single-nucleotide polymorphism; SNP; Triticum aestivum; Triticum durum; variant annotation; Wheat; whole-genome sequencing; variant annotation; rapid generation advance; SNP; whole-genome sequencing; hst1; Na+ accumulation; salt tolerant
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms20102585

Salinity critically limits rice metabolism, growth, and productivity worldwide. Improvement of the salt resistance of locally grown high-yielding cultivars is a slow process. The objective of this study was to develop a new salt-tolerant rice germplasm using speed-breeding. Here, we precisely introgressed the
gene, transferring salinity tolerance from "Kaijin" into high-yielding "Yukinko-mai" (WT) rice through single nucleotide polymorphism (SNP) marker-assisted selection. Using a biotron speed-breeding technique, we developed a BC
F
population, named "YNU31-2-4", in six generations and 17 months. High-resolution genotyping by whole-genome sequencing revealed that the BC
F
genome had 93.5% similarity to the WT and fixed only 2.7% of donor parent alleles. Functional annotation of BC
F
variants along with field assessment data indicated that "YNU31-2-4" plants carrying the
gene had similar agronomic traits to the WT under normal growth condition. "YNU31-2-4" seedlings subjected to salt stress (125 mM NaCl) had a significantly higher survival rate and increased shoot and root biomasses than the WT. At the tissue level, quantitative and electron probe microanalyzer studies indicated that "YNU31-2-4" seedlings avoided Na
accumulation in shoots under salt stress. The "YNU31-2-4" plants showed an improved phenotype with significantly higher net CO
assimilation and lower yield decline than WT under salt stress at the reproductive stage. "YNU31-2-4" is a potential candidate for a new rice cultivar that is highly tolerant to salt stress at the seedling and reproductive stages, and which might maintain yields under a changing global climate.