Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice

Abstract

Nitrogen-use efficiency (NUE) is a function of N-response and yield that is controlled by many genes and phenotypic parameters that are poorly characterized. This study compiled all known yield-related genes in rice and mined them from the N-responsive microarray data to find 1,064 NUE-related genes. Many of them are novel genes hitherto unreported as related to NUE, including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases. They were further shortlisted to 62 NUE-candidate genes following hierarchical methods, including quantitative trait locus (QTL) co-localization, functional evaluation in the literature, and protein–protein interactions (PPIs). They were localized to chromosomes 1, 3, 5, and 9, of which chromosome 1 with 26 genes emerged as a hotspot for NUE spanning 81% of the chromosomes. Further, co-localization of the NUE genes on NUE-QTLs resolved differences in the earlier studies that relied mainly on N-responsive genes regardless of their role in yield. Functional annotations and PPIs for all the 1,064 NUE-related genes and also the shortlisted 62 candidates revealed transcription, redox, phosphorylation, transport, development, metabolism, photosynthesis, water deprivation, and hormonal and stomatal function among the prominent processes. In silico expression analysis confirmed differential expression of the 62 NUE-candidate genes in a tissue/stage-specific manner. Experimental validation in two contrasting genotypes revealed that high NUE rice shows better photosynthetic performance, transpiration efficiency and internal water-use efficiency in comparison to low NUE rice. Feature Selection Analysis independently identified one-third of the common genes at every stage of hierarchical shortlisting, offering 6 priority targets to validate for improving the crop NUE.

Comparative Transcriptomic Analyses of Nitrate-Response in Rice Genotypes With Contrasting Nitrogen Use Efficiency Reveals Common and Genotype-Specific Processes, Molecular Targets and Nitrogen Use Efficiency-Candidates

“…Nitrogen use efficiency genes were defined as N-responsive and yield-related genes, as reported by Kumari et al (2021) . The yield-related genes reported therein were further updated from literature and databases and used for Venn selection with the N-responsive DEGs identified in the genotypes Nidhi and Panvel1 to obtain the NUE genes in them.…”

“…The yield-related genes reported therein were further updated from literature and databases and used for Venn selection with the N-responsive DEGs identified in the genotypes Nidhi and Panvel1 to obtain the NUE genes in them. Similarly, NUE-QTLs reported therein were further updated from literature and the NUE genes identified in Nidhi and Panvel1 were co-localized onto NUE-QTLs as described by Kumari et al (2021) .…”

“…This is evidenced by genome sequences of 3000 rice genotypes ( Li et al, 2014 ) and growing functional genomics of N ( Li et al, 2018 ; Pathak et al, 2020 ; Mandal et al, 2022 ). Further, the recent NUE phenotype ( Sharma et al, 2018 , 2021 ; Pathak et al, 2021 ) growing quantitative trait loci (QTL) and genotyping ( Kumari et al, 2021 ) make rice an ideal target crop for NUE improvement. A recent simulation showed that $743 million per year could be saved by a 20% increase in rice NUE ( Langholtz et al, 2021 ), while the global expenditure in that direction is not even a tiny fraction of it.…”

“…However, soil microbial conversions ensure that nitrate is the predominant form of N available to all crops including rice, regardless of the form of N-supply ( Coskun et al, 2017 ). This is one of the reasons why nitrate-transcriptomes are predominant even in the rice functional genomics literature (listed in Kumari et al, 2021 ). They are also available for subspecies Indica ( Pathak et al, 2020 ) and Japonica ( Mandal et al, 2022 ).…”

“…In rice, several genes such as OsGRF4, OsDof1, NADH-GOGAT, OsNPF6.1, OsNRT2.3b, OsNRT2.1, OsPTR9, OsNPF8.20, OsNRT1.1A, OsFBP1 have been reported to increase NUE ( Kumari et al, 2021 and references cited therein) including alanine aminotransferase ( Good et al, 2007 ), OsPTR9 ( Fang et al, 2013 ), and DEP1 ( Sun et al, 2014 ). In addition to these genes, some interesting QTLs have been identified as linked to NUE ( Sinha et al, 2018 ; Waqas et al, 2018 ; Kumari et al, 2021 ). Transcriptomic studies in rice revealed thousands of nitrate-responsive genes totaling 23,626 numbers ( Mandal et al, 2022 ) but they were all limited to single genotypes.…”