Identification of bHLH genes through genome-wide association study and antisense expression of ZjbHLH076/ZjICE1 influence tolerance to low temperature and salinity in Zoysia japonica

Abstract Background: Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there were limited studies focusing on cold tolerance at the bud burst stage, therefore, considerable attention should be paid to the genetic basis of cold tolerance at the bud burst stage (CTBB).Results: In this study, a natural population consisting of 211 rice landraces collected from 15 provinces of China and other countries were firstly used to evaluate the cold tolerance at the bud burst stage. Population structure analysis showed that this population divided into three groups and was rich in genetic diversity. Our evaluation results confered that the japonica rice was more tolerance to cold at the bud burst stage than indica rice. Genome-wide association study (GWAS) were performed through the phenotypic data of 211 rice landraces and 36,727 SNPs dataset under a mixed linear model, and 12 QTLs (P < 0.0001) were identified according to the seedling survival rate (SSR) treated at 4 ℃, in which there are five QTLs (qSSR2-2, qSSR3-1, qSSR3-2, qSSR3-3 and qSSR9) which were co-located with previous studies, and seven QTLs (qSSR2-1, qSSR3-4, qSSR3-5, qSSR3-6, qSSR3-7, qSSR4 and qSSR7) which were reported for the first time. Among these QTLs, qSSR9, harboring the highest-peak SNP, explained biggest phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were nominated as candidates for qSSR9. Conclusion: This natural population consisting of 211 rice landraces with high density SNPs will serve as a better choice for identifying rice QTLs/genes in future, and the detected QTLs associated with cold tolerance in rice bud burst stage will be conducive to further mining favorable genes and breeding of rice varieties under cold stress.

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Assessment of cold stress tolerance in maize through quantitative trait locus, genome-wide association study and transcriptome analysis

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha49412525 ◽

2021 ◽

Vol 49 (4) ◽

pp. 12525

Author(s):

Syed F.A. GILLANI ◽

Adnan RASHEED ◽

Gai YUHONG ◽

Wei JIAN ◽

Wang Y. XIA ◽

...

Keyword(s):

Low Temperature ◽

Association Study ◽

Temperature Stress ◽

Genome Wide Association Study ◽

Grain Filling ◽

Low Temperature Stress ◽

Genome Wide Association ◽

Ps Ii ◽

Genome Wide ◽

Trait Locus

Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype phenotype associations in many species thanks to advances in next-generation sequencing (NGS) technologies. Maize is an ideal crop for GWAS and significant progress has been made in the last decade. This review summarizes current GWAS efforts in maize functional genomics research and discusses future prospects in the omics era. The general goal of GWAS is to link genotypic variations to corresponding differences in phenotype using the most appropriate statistical model in a given population. The current review also presents perspectives for optimizing GWAS design and analysis. GWAS analysis of data from RNA, protein, and metabolite-based omics studies is discussed, along with new models and new population designs that will identify causes of phenotypic variation that have been hidden to date. The detailed that low temperature in maize seedlings altogether restricts germination and seedlings' development and destabilizes the cancer prevention agent safeguard component. Cold pressure adversely influences root morphology, photosystem II (PS II) effectiveness, chlorophyll substance, and leaf region. A short scene of low temperature stress (for example, under 10 °C for 7 days) during the V6–V9 maize development stages can fundamentally defer the anthesis commencement. Among the morphological reactions by focused on maize plants, low temperature stress causes strange tuft development in maize, along these lines influencing the fertilization and grain filling measures. Hence, problematic temperatures can cause a genuine yield decrease if happening at basic conceptive stages, as plants allocate over half of their photosynthesis to foster grains during this stage until physiological development. Low temperature stress fundamentally diminishes the plant stature and absolute yield biomass of maize. Leaf improvement turns out to be delayed in chilly focused on plants because of a drawn-out cell cycle and diminished pace of mitosis. The joint and continuous efforts of the whole community will enhance our understanding of maize quantitative traits and boost crop molecular breeding designs.

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