Screening and classification of genotypes for seedling-stage chilling stress tolerance in rice and validation of the trait using SSR markers

Abstract

Low-temperature stress is an important factor affecting the growth and development of rice in temperate and high-elevation areas. In this study, 220 germplasm lines were used for screening of tolerant genotypes, validation of molecular markers and identification of robust markers for seedling-stage chilling stress tolerance to be used in marker-assisted breeding (MAS) programme. The temperature regimes imposed in the growth chamber simulated cold-stress injuries at the seedling stages of the germplasm lines. The genotypes were classified into six classes: those having susceptible genotypes were classified into moderately and highly susceptible types, while tolerant types into moderately tolerant, tolerant, highly tolerant and very highly tolerant classes. Genotypes namely Langma, Umleng-1 and Geetanjali showed survival up to 25 d, which were better than the positive check Kalinga-III surviving up to 20 d under chilling stress. Ten simple sequence repeat (SSR) markers were tested for differentiation of genotypes. Individual use of SSR markers like RM284, RM286, RM85, RM341 and RM5746 can be applied in MAS breeding including combination use of non-pair markers like RM284, RM239 and RM85, which was even better than the combined use of RM284 and RM85. However, combined use of all ten markers can most effectively be employed for cold tolerance through MAS breeding.

Genes, pathways and transcription factors involved in seedling stage chilling stress tolerance in indica rice through RNA-Seq analysis

“…However, rice genotypes classification with respect to seedling stage cold tolerance by exposing the seedlings to a temperature regime of 25 to 4 °C and further extending the exposure up to 15, 20 and 25 days at 4 °C were reported in previous study where the rice genotypes were grouped into six classes [2, 3]. Rice genotype, Geetanjali was categorized as very highly tolerant and Sahabhagidhan as highly susceptible type to chilling stress reported by earlier publications [2, 3]. Thus, both the studied genotypes for RNA-seq analyses were confirmed to be very highly contrasting for seedling stage chilling stress tolerance.…”

“…The RNA-seq technology has true advantage of representing the global transcriptome, which is limited in microarray since it depends on predefined probes. Rice genotype, Geetanjali was categorized as very highly tolerant and Sahabhagidhan as highly susceptible type to chilling stress reported by earlier publications [2–4]. The highly tolerant genotype Geetanjali could survive upto 25 days under chilling stress of 4 °C.…”

“…Now-a-days, the extent of unexpected cold weather has increased due to extreme weather events. The yield of rice in Australia, Korea, India, China, Japan and many other countries is affected by cold stress [2, 3, 6]. The dry season rice of India particularly boro rice faces cold stress during seedling stage.…”

Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice

“…Genotypes were screened following the published protocol for chilling stress tolerance (Pradhan et al, 2015). As per the protocol, seedlings were grown in RGA-cum-Phytotron till three-leaf stage set at 25°C temperature and photoperiod of 12 h. At this stage, the weak seedlings were removed and healthy seedlings were exposed to low temperature regime (LTR) treatments in the growth chamber with a setting of 75–85% relative humidity and 800 μ moles s −1 m −2 light intensity.…”

Integrated RNA-seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots

“…The reduction of rice yield caused by cold stress has been a common problem in the world [2][3][4], especially in China, Japan, Australia, Korea, India, etc. [5][6][7].…”