Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

Identifications of Genes Involved in ABA and MAPK Signaling Pathways Positively Regulating Cold Tolerance in Rice

Cold stress (CS) significantly impacts rice (Oryza sativa L.) growth during seedling and heading stages. Based on two-year field observations, this study identified two rice lines, L9 (cold stress-sensitive) and LD18 (cold stress-tolerant), showing contrasting CS responses. L9 exhibited a 38% reduction in photosynthetic efficiency, whereas LD18 remained unchanged, correlating with seed rates. Transcriptome analysis identified differentially expressed genes (DEGs) with LD18 showing enriched pathways (carbon fixation, starch/sucrose metabolism, and glutathione metabolism). LD18 displayed dramatically enhanced expression of MAPK-related genes (LOC4342017, LOC9267741, and LOC4342267) and increased ABA signaling genes (LOC4333690, LOC4345611, and LOC4335640) compared with L9 exposed to CS. Results from qPCR confirmed the enhanced expression of the three MAPK-related genes in LD18 with a dramatic reduction in L9 under CS relative to that under CK. We also observed up to 66% reduction in expression levels of the three genes related to the ABA signaling pathway in L9 relative to LD18 under CS. Consistent with the results of photosynthetic efficiency, metabolic analysis suggests pyruvate metabolism, TCA cycle, and carbon metabolism enrichment in LD18 under CS. The study reveals reprogramming of the carbon assimilation metabolic pathways, emphasizing the critical roles of the key DEGs involved in ABA and MAPK signaling pathways in positive regulation of LD18 response to CS, offering the foundation toward cold tolerance breeding through targeted gene editing.

The seed endophytic microbe Microbacterium testaceum M15 enhances the cold tolerance and growth of rice (Oryza sativa L.)

The potential of seed endophytic microbes to enhance plant growth and resilience is well recognized, yet their role in alleviating cold stress in rice remains underexplored due to the complexity of these microbial communities. In this study, we investigated the diversity of seed endophytic microbes in two rice varieties, the cold-sensitive CB9 and the cold-tolerant JG117. Our results revealed significant differences in the abundance of Microbacteriaceae, with JG117 exhibiting a higher abundance under both cold stress and room temperature conditions compared to CB9. Further analysis led to the identification of a specific cold-tolerant microbe, Microbacterium testaceum M15, in JG117 seeds. M15-inoculated CB9 plants showed enhanced growth and cold tolerance, with a germination rate increase from 40 % to 56.67 % at 14℃ and a survival rate under cold stress (4℃) doubling from 22.67 % to 66.67 %. Additionally, M15 significantly boosted chlorophyll content by over 30 %, increased total protein by 16.31 %, reduced malondialdehyde (MDA) levels by 37.76 %, and increased catalase activity by 26.15 %. Overall, our study highlights the potential of beneficial endophytic microbes like M. testaceum M15 in improving cold tolerance in rice, which could have implications for sustainable agricultural practices and increased crop productivity in cold-prone regions.

Comparative transcriptome analysis and meta-QTLs mapping reveal the regulatory mechanism of cold tolerance in rice at the budding stage

Rice (Oryza sativa L.) is one of the most extensively farmed food crops, but its development and productivity are significantly impacted by cold stress during the budding period. In this study, transcriptome sequencing was conducted on two types of rice: the cold-sensitive indica rice A117 and the substantially cold-tolerant japonica rice B106 under control and cold treatments. Differentially expressed genes between the two materials under cold conditions were analyzed using GO and KEGG enrichment analyses. The results revealed that processes such as the TCA cycle, glycolysis/glycogenesis, oxidative phosphorylation, and glutathione metabolism contribute to B106's cold tolerance. Additionally, an enrichment analysis of cold-induced genes in each material and shared genes identified significant enrichment in pathways such as glutathione metabolism, phenylpropanoid biosynthesis, and photosynthesis-antenna proteins. Initial cold tolerance QTLs at the rice bud stage were collected from published literature, and meta-QTL mapping identified 9 MQTLs. Gene expression profiling led to the identification of 75 potential DEGs within the 9 MQTLs region, from which four candidate genes (Os02g0194100, Os03g0802500, Os05g0129000, and Os07g0462000) were selected using qRT-PCR and gene annotation. These findings provide genetic resources for further research on the molecular mechanisms underlying rice's response to cold stress during the bud stage.

Uncovering Novel QTLs and Candidate Genes for Salt Tolerance at the Bud Burst Stage in Rice through Genome-Wide Association Study

Salt stress is one of the most important factors limiting rice growth and yield increase. Salt tolerance of rice at the bud burst (STB) stage determines whether germinated seeds can grow normally under salt stress, which is very important for direct seeding. However, reports on quantitative trait loci (QTLs) and candidate genes for STB in rice are very limited. In this study, a natural population of 130 indica and 81 japonica rice accessions was used to identify STB-related QTLs and candidate genes using a genome-wide association study (GWAS). Nine QTLs, including five for relative shoot length (RSL), two for relative root length (RRL), and two for relative root number (RRN), were identified. Five of these STB-related QTLs are located at the same site as the characterized salt tolerance genes, such as OsMDH1, OsSRFP1, and OsCDPK7. However, an important QTL related to RSL, qRSL1-2, has not been previously identified and was detected on chromosome 1. The candidate region for qRSL1-2 was identified by linkage disequilibrium analysis, 18 genes were found to have altered expression levels under salt stress through the RNA-seq database, and 10 of them were found to be highly expressed in the shoot. It was also found that, eight candidate genes (LOC_Os01g62980, LOC_Os01g63190, LOC_Os01g63230, LOC_Os01g63280, LOC_Os01g63400, LOC_Os01g63460, and LOC_Os01g63580) for qRSL1-2 carry different haplotypes between indica and japonica rice, which exactly corresponds to the significant difference in RSL values between indica and japonica rice in this study. Most of the accessions with elite haplotypes were indica rice, which had higher RSL values. These genes with indica-japonica specific haplotypes were identified as candidate genes. Rice accessions with elite haplotypes could be used as important resources for direct seeding. This study also provides new insights into the genetic mechanism of STB.

Genetic dissection of cold tolerance at the budding stage of rice in an indica-japonica recombination inbred line population

Rice is highly cold-sensitive, and thus, the promotion of cold resistance in buds is essential. In this study, we conducted a mapping analysis to identify quantitative trait loci (QTLs) associated with cold tolerance in buds. The analysis was performed using a recombinant inbred line (RIL) population consisting of 192 lines derived from the cold-tolerant strain 02428 and the cold-sensitive strain YZX. Seven additive loci on chromosomes 1, 4, 5, and 6 were identified, of which loci 3 and 7 were found in two crop seasons, indicating stability. Three epistatic interactions, one present over two seasons, were found. Loci 3 and 7 pyramided with two main-effect QTLs observed to control the rate of low-temperature germination in our previous study. Two materials with good cold resistance at the germination and bud stages were obtained, namely, G93 and G146. Transcriptome sequencing analysis of the two parent buds after cold treatment found that genes expressed differentially between the two parents were related to photosynthesis, energy metabolism, and reactive oxygen scavenging. Five candidate genes, namely, Os01g0385400, Os01g0388000, Os06g0287700, Os06g0289200, and Os06g0291100, were selected in the two stable intervals based on gene expression profiles and annotations. These genetic loci exhibit strong potential as targets for breeding cold tolerance in buds and require additional investigation. In conclusion, this work provides valuable genetic resources that can be utilized to improve the cold tolerance of rice.

Research advance on cold tolerance in chrysanthemum

Chrysanthemums are one of the top ten most well-known traditional famous flowers in China and one of the top four cut flowers worldwide, holding a significant position in landscape gardening. The cold temperatures of winter restrict the cultivation, introduction, and application of chrysanthemum, resulting in high costs for year-round production. This severely impacts the ornamental and economic value of chrysanthemum. Therefore, research on cold tolerance is of vital importance for guiding chrysanthemum production and application. With the development of genomics, transcriptomics, metabolomics, and other omics approaches, along with high-throughput molecular marker technologies, research on chrysanthemum cold tolerance has been continuously advancing. This article provides a comprehensive overview of the progress in cold tolerance research from various aspects, including chrysanthemum phenotype, physiological mechanisms, the forward genetics, molecular mechanisms, and breeding. The aim is to offer insights into the mechanisms of cold tolerance in chrysanthemum and provide reference for in-depth research and the development of new cold tolerance chrysanthemum varieties.

Transcriptome Analysis of the Responses of Rice Leaves to Chilling and Subsequent Recovery

Improving chilling tolerance at the seedling stage in rice is essential for agricultural research. We combined a physiological analysis with transcriptomics in a variety Dular subjected to chilling followed by recovery at normal temperature to better understand the chilling tolerance mechanisms of rice. Chilling inhibited the synthesis of chlorophyll and non-structural carbohydrate (NSC) and disrupted the ion balance of the plant, resulting in the impaired function of rice leaves. The recovery treatment can effectively reverse the chilling-related injury. Transcriptome results displayed that 21,970 genes were identified at three different temperatures, and 11,732 genes were differentially expressed. According to KEGG analysis, functional categories for differentially expressed genes (DEGs) mainly included ribosome (8.72%), photosynthesis–antenna proteins (7.38%), phenylpropanoid biosynthesis (11.41%), and linoleic acid metabolism (10.07%). The subcellular localization demonstrated that most proteins were located in the chloroplasts (29.30%), cytosol (10.19%), and nucleus (10.19%). We proposed that some genes involved in photosynthesis, ribosome, phenylpropanoid biosynthesis, and linoleic acid metabolism may play key roles in enhancing rice adaptation to chilling stress and their recovery capacity. These findings provide a foundation for future research into rice chilling tolerance mechanisms.

ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress

Low temperature is one of the important environmental factors that affect rice growth and yield. To better understand the japonica rice responses to cold stress, isobaric tags for a relative and absolute quantification (iTRAQ) labeling-based quantitative proteomics approach was used to detected changes in protein levels. Two-week-old seedlings of the cold tolerant rice variety Kongyu131 were treated at 8°C for 24, 48 and 72 h, then the total proteins were extracted from tissues and used for quantitative proteomics analysis. A total of 5082 proteins were detected for quantitative analysis, of which 289 proteins were significantly regulated, consisting of 169 uniquely up-regulated proteins and 125 uniquely down-regulated proteins in cold stress groups relative to the control group. Functional analysis revealed that most of the regulated proteins are involved in photosynthesis, metabolic pathway, biosynthesis of secondary metabolites and carbon metabolism. Western blot analysis showed that protein regulation was consistent with the iTRAQ data. The corresponding genes of 25 regulated proteins were used for quantitative real time PCR analysis, and the results showed that the mRNA level was not always parallel to the corresponding protein level. The importance of our study is that it provides new insights into cold stress responses in rice with respect to proteomics and provides candidate genes for cold-tolerance rice breeding.

Chilling tolerance in rice: Past and present

Rice is generally sensitive to chilling stress, which seriously affects growth and yield. Since early in the last century, considerable efforts have been made to understand the physiological and molecular mechanisms underlying the response to chilling stress and improve rice chilling tolerance. Here, we review the research trends and advances in this field. The phenotypic and biochemical changes caused by cold stress and the physiological explanations are briefly summarized. Using published data from the past 20 years, we reviewed the past progress and important techniques in the identification of quantitative trait loci (QTL), novel genes, and cellular pathways involved in rice chilling tolerance. The advent of novel technologies has significantly advanced studies of cold tolerance, and the characterization of QTLs, key genes, and molecular modules have sped up molecular design breeding for cold tolerance in rice varieties. In addition to gene function studies based on overexpression or artificially generated mutants, elucidating natural allelic variation in specific backgrounds is emerging as a novel approach for the study of cold tolerance in rice, and the superior alleles identified using this approach can directly facilitate breeding.

Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS

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 have been limited studies focusing on cold tolerance at the bud burst stage; therefore, considerable attention should be given to the genetic basis of cold tolerance at this stage.

RESULTS

In this study, a natural population consisting of 211 rice landraces collected from 15 provinces in China and other countries was used for the first time to evaluate cold tolerance at the bud burst stage. Population structure analysis showed that this population was divided into two groups and was rich in genetic diversity. Our evaluation results confirmed that japonica rice was more tolerant to cold at the bud burst stage than indica rice. A genome-wide association study (GWAS) was performed with the phenotypic data of 211 rice landraces and a 36,727 SNP dataset under a mixed linear model. Twelve QTLs (P < 0.0001) were identified for the seedling survival rate (SR) after treatment at 4 °C, in which there were five QTLs (qSR2-2, qSR3-1, qSR3-2, qSR3-3 and qSR9) that were colocalized with those from previous studies and seven QTLs (qSR2-1, qSR3-4, qSR3-5, qSR3-6, qSR3-7, qSR4 and qSR7) that were reported for the first time. Among these QTLs, qSR9, harboring the most significant SNP, explained the most phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were identified as candidates for qSR9.

CONCLUSION

This natural population consisting of 211 rice landraces combined with high-density SNPs will serve as a better choice for identifying rice QTLs/genes in the future, and the detected QTLs associated with cold tolerance at the bud burst stage in rice will be conducive to further mining favorable genes and breeding rice varieties under cold stress.

Identification of Candidate Genes Conferring Cold Tolerance to Rice (Oryza sativa L.) at the Bud-Bursting Stage Using Bulk Segregant Analysis Sequencing and Linkage Mapping

Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice. The identification of cold-tolerance quantitative trait loci (QTL) in species that can stably tolerate cold environments is crucial for the molecular breeding of rice with such traits. In our study, high-throughput QTL-sequencing analyses were performed in a 460-individual F_{2 : 3} mapping population to identify the major QTL genomic regions governing cold tolerance at the bud-bursting (CTBB) stage in rice. A novel major QTL, qCTBB9, which controls seed survival rate (SR) under low-temperature conditions of 5°C/9 days, was mapped on the 5.40-Mb interval on chromosome 9. Twenty-six non-synonymous single-nucleotide polymorphism (nSNP) markers were designed for the qCTBB9 region based on re-sequencing data and local QTL mapping conducted using traditional linkage analysis. We mapped qCTBB9 to a 483.87-kb region containing 58 annotated genes, among which six predicted genes contained nine nSNP loci. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed that only Os09g0444200 was strongly induced by cold stress. Haplotype analysis further confirmed that the SNP 1,654,225 bp in the Os09g0444200 coding region plays a key role in regulating the cold tolerance of rice. These results suggest that Os09g0444200 is a potential candidate for qCTBB9. Our results are of great significance to explore the genetic mechanism of rice CTBB and to improve the cold tolerance of rice varieties by marker-assisted selection.

Genome-wide association study reveals novel genetic loci contributing to cold tolerance at the germination stage in indica rice

Low temperature at the germination stage is one of the major abiotic stresses limiting rice (Oryza sativa L.) production, especially in regions where rice seeds are sown directly. However, few relevant genetic loci and genes have been identified. In this study, we report the phenotypic analysis of low temperature germination (LTG) in 200 indica rice varieties and a genome-wide association study (GWAS) of LTG in this collection using 161,657 high-quality SNPs, which were identified via genotyping-by-sequencing (GBS) of all the rice varieties. A total of 159 genetic loci were detected, and they were evenly distributed on all 12 chromosomes. Among them, 51 loci were detected more than twice; in particular, 23 loci were detected repeatedly in both the wet and dry seasons, and 569 genes were predicted in the 200-kb genomic region harbouring these 23 loci. Furthermore, 14,742 differentially expressed genes (DEGs) were identified using RNA sequencing. By integrating GWAS and RNA sequencing, 179 candidate DEGs were obtained. Sequence variation in the region of loci 95 was analyzed using 20 varieties with extreme phenotype. The polymorphisms of three DEGs (Os07g0585500, Os07g0585700, Os07g0585900) were associated with their phenotypes. Haplotype analysis of the three genes demonstrated that almost all the varieties with the same haplotype as japonica Nipponbare on the three DEGs showed high LTG ability. These findings provide valuable information for understanding the genetic control of LTG and performing molecular breeding with marker-assisted selection in indica rice.

The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice (Oryza sativa L.)

BACKGROUND

Direct seeding is an efficient cultivation technique in rice. However, poor low temperature germinability (LTG) of modern rice cultivars limits its application. Identifying the genes associated with LTG and performing molecular breeding is the fundamental way to address this issue. However, few LTG QTLs have been fine mapped and cloned so far.

RESULTS

In the present study, the LTG evaluation of 375 rice accessions selected from the Rice Diversity Panel 2 showed that there were large LTG variations within the population, and the LTG of Indica group was significantly higher than that of Japonica and Aus groups (p < 0.01). In total, eleven QTLs for LTG were identified through genome-wide association study (GWAS). Among them, qLTG_sRDP2-3/qLTG_JAP-3, qLTG_AUS-3 and qLTG_sRDP2-12 are first reported in the present study. The QTL on chromosome 10, qLTG_sRDP2-10a had the largest contribution to LTG variations in 375 rice accessions, and was further validated using single segment substitution line (SSSL). The presence of qLTG_sRDP2-10a could result in 59.8% increase in LTG under 15 °C low temperature. The expression analysis of the genes within qLTG_sRDP2-10a region indicated that LOC_Os10g22520 and LOC_Os10g22484 exhibited differential expression between the high and low LTG lines. Further sequence comparisons revealed that there were insertion and deletion sequence differences in the promoter and intron region of LOC_Os10g22520, and an about 6 kb variation at the 3' end of LOC_Os10g22484 between the high and low LTG lines, suggesting that the sequence variations of the two genes could be the cause for their differential expression in high and low LTG lines.

CONCLUSION

Among the 11 QTLs identified in this study, qLTG_sRDP2-10a could also be detected in other three studies using different germplasm under different cold environments. Its large effect and stable expression make qLTG_sRDP2-10a particularly valuable in rice breeding. The two genes, LOC_Os10g22484 and LOC_Os10g22520, were considered as the candidate genes underlying qLTG_sRDP2-10a. Our results suggest that integrating GWAS and SSSL can facilitate identification of QTL for complex traits in rice. The identification of qLTG_sRDP2-10a and its candidate genes provide a promising source for gene cloning of LTG and molecular breeding for LTG in rice.

Genome-Wide Association Study of Rice Rooting Ability at the Seedling Stage

BACKGROUND

Rice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability.

RESULTS

To characterize the genetic basis for rice rooting ability, we used a natural rice population, genotyped by a 90 K single nucleotide polymorphism (SNP) array, to identify the loci associated with rooting-related traits through the genome-wide association study (GWAS). Population structure analysis divided the natural population into two subgroups: indica and japonica. We measured four traits for evaluating rice rooting ability, namely root growth ability (RGA), maximum root length (MRL), root length (RL), and root number (RN). Using the association study in three panels consisting of one for the full population, one for indica, and one for japonica, 24 SNPs associated with rooting ability-related traits were identified. Through comparison of the relative expression levels and DNA sequences between germplasm with extreme phenotypes, results showed that LOC_Os05g11810 had non-synonymous variations at the coding region, which may cause differences in root number, and that the expression levels of LOC_Os04g09900 and LOC_Os04g10060 are closely associated with root length variation.

CONCLUSIONS

Through evaluation of the rice rooting ability-related traits and the association mapping, we provided useful information for understanding the genetic basis of rice rooting ability and also identified some candidate genes and molecular markers for rice root breeding.

Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

An attempt was made in the current study to identify the main-effect and co-localized quantitative trait loci (QTLs) for germination and early seedling growth traits under low-temperature stress (LTS) conditions in rice. The plant material used in this study was an early backcross population of 230 introgression lines (ILs) in BCIF7 generation derived from the Weed Tolerant Rice-1 (WTR-1) (as the recipient) and Haoannong (HNG) (as the donor). Genetic analyses of LTS tolerance revealed a total of 27 main-effect quantitative trait loci (M-QTLs) mapped on 12 chromosomes. These QTLs explained more than 10% of phenotypic variance (PV), and average PV of 12.71% while employing 704 high-quality SNP markers. Of these 27 QTLs distributed on 12 chromosomes, 11 were associated with low-temperature germination (LTG), nine with low-temperature germination stress index (LTGS), five with root length stress index (RLSI), and two with biomass stress index (BMSI) QTLs, shoot length stress index (SLSI) and root length stress index (RLSI), seven with seed vigor index (SVI), and single QTL with root length (RL). Among them, five significant major QTLs (qLTG(I) 1 , qLTGS(I) 1-2 , qLTG(I) 5 , qLTGS(I) 5 , and qLTG(I) 7 ) mapped on chromosomes 1, 5, and 7 were associated with LTG and LTGS traits and the PV explained ranged from 16 to 23.3%. The genomic regions of these QTLs were co-localized with two to six QTLs. Most of the QTLs were growth stage-specific and found to harbor QTLs governing multiple traits. Eight chromosomes had more than four QTLs and were clustered together and designated as promising LTS tolerance QTLs (qLTTs), as qLTT 1 , qLTT 2 , qLTT 3 , qLTT 5 , qLTT 6 , qLTT 8 , qLTT 9 , and qLTT 11 . A total of 16 putative candidate genes were identified in the major M-QTLs and co-localized QTL regions distributed on different chromosomes. Overall, these significant genomic regions of M-QTLs are responsible for multiple traits and this suggested that these could serve as the best predictors of LTS tolerance at germination and early seedling growth stages. Furthermore, it is necessary to fine-map these regions and to find functional markers for marker-assisted selection in rice breeding programs for cold tolerance.

Chemical and Transcriptomic Analysis of Cuticle Lipids under Cold Stress in Thellungiella salsuginea

Plant cuticle lipids form outer protective layers to resist environmental stresses; however, the relationship between cuticle properties and cold tolerance is unclear. Here, the extremophyte Thellungiella salsuginea was stressed under cold conditions (4 °C) and the cuticle of rosette leaves was examined in terms of epicuticular wax crystal morphology, chemical composition, and cuticle-associated gene expression. The results show that cold induced formation of distinct lamellas within the cuticle ultrastructure. Cold stress caused 14.58% and 12.04% increases in the amount of total waxes and cutin monomer per unit of leaf area, respectively, probably associated with the increase in total fatty acids. The transcriptomic analysis was performed on rosette leaves of Thellungiella exposed to cold for 24 h. We analyzed the expression of 72 genes putatively involved in cuticle lipid metabolism, some of which were validated by qRT-PCR (quantitative reverse transcription PCR) after both 24 h and one week of cold exposure. Most cuticle-associated genes exhibited higher expression levels under cold conditions, and some key genes increased more dramatically over the one week than after just 24 h, which could be associated with increased amounts of some cuticle components. These results demonstrate that the cuticle provides some aspects of cold adaptation in T. salsuginea.

Finger Millet [Eleusine coracana (L.) Gaertn.] Improvement: Current Status and Future Interventions of Whole Genome Sequence

The whole genome sequence (WGS) of the much awaited, nutrient rich and climate resilient crop, finger millet (Eleusine coracana (L.) Gaertn.) has been released recently. While possessing superior mineral nutrients and excellent shelf life as compared to other major cereals, multiploidy nature of the genome and relatively small plantation acreage in less developed countries hampered the genome sequencing of finger millet, disposing it as one of the lastly sequenced genomes in cereals. The genomic information available for this crop is very little when compared to other major cereals like rice, maize and barley. As a result, only a limited number of genetic and genomic studies has been undertaken for the improvement of this crop. Finger millet is known especially for its superior calcium content, but the high-throughput studies are yet to be performed to understand the mechanisms behind calcium transport and grain filling. The WGS of finger millet is expected to help to understand this and other important molecular mechanisms in finger millet, which may be harnessed for the nutrient fortification of other cereals. In this review, we discuss various efforts made so far on the improvement of finger millet including genetic improvement, transcriptome analysis, mapping of quantitative trait loci (QTLs) for traits, etc. We also discuss the pitfalls of modern genetic studies and provide insights for accelerating the finger millet improvement with the interventions of WGS in near future. Advanced genetic and genomic studies aided by WGS may help to improve the finger millet, which will be helpful to strengthen the nutritional security in addition to food security in the developing countries of Asia and Africa.