Molecular dissection of seedling-vigor and associated physiological traits in rice

A Novel Function of GW5 on Controlling the Early Growth Vigor and its Haplotype Effect on Shoot Dry Weight and Grain Size in Rice (Oryza sativa L.)

Strong early growth vigor is an essential target in both direct seeded rice breeding and high-yielding rice breeding for rice varieties with relatively short growth duration in the double-cropping region. Shoot dry weight (SDW) is one of the important traits associated with early growth vigor, and breeders have been working to improve this trait. Finding stable QTLs or functional genes for SDW is crucial for improving the early growth vigor by implementing molecular breeding in rice. Here, a genome-wide association analysis revealed that the QTL for SDW, qSDW-5, was stably detected in the three cultivation methods commonly used in production practice. Through gene-based haplotype analysis of the annotated genes within the putative region of qSDW-5, and validated by gene expression and knockout transgenic experiments, LOC_Os05g09520, which is identical to the reported GW5/GSE5 controlling grain width (GW) and thousand grain weight (TGW) was identified as the causal gene for qSDW-5. Five main haplotypes of LOC_Os05g09520 were identified in the diverse international rice collection used in this study and their effects on SDW, GW and TGW were analyzed. Phenotypic comparisons of the major haplotypes of LOC_Os05g09520 in the three subpopulations (indica, japonica and aus) revealed the same patterns of wider GW and higher TGW along with higher SDW. Furtherly, the haplotype analysis of 138 rice varieties/lines widely used in southern China showed that 97.8% of the cultivars/lines carry Hap2LOC_Os05g09520. These results not only provide a promising gene source for the molecular breeding of rice varieties with strong early growth vigor, but also elucidate the effect of the LOC_Os05g09520 haplotypes on SDW, GW, and TGW in rice. Importantly, this study provides direct genetic evidence that these three traits are significantly correlated, and suggests a breeding strategy for developing high-yielding and slender grain-shaped indica cultivars with strong early growth vigor.

Genetic dissection of Brassica napus seed vigor after aging

KEY MESSAGE

Stable and novel QTLs that affect seed vigor under different storage durations were discovered, and BnaOLE4, located in the interval of cqSW-C2-3, increased seed vigor after aging. Seed vigor is an important trait in crop breeding; however, the underlying molecular regulatory mechanisms governing this trait in rapeseed remain largely unknown. In the present study, vigor-related traits were analyzed in seeds from a doubled haploid (DH) rapeseed (Brassica napus) population grown in 2 different environments using seeds stored for 7, 5, and 3 years under natural storage conditions. A total of 229 quantitative trait loci (QTLs) were identified and were found to explain 3.78%-17.22% of the phenotypic variance for seed vigor-related traits after aging. We further demonstrated that seed vigor-related traits were positively correlated with oil content (OC) but negatively correlated with unsaturated fatty acids (FAs). Some pleiotropic QTLs that collectively regulate OC, FAs, and seed vigor, such as uq.A8, uq.A3-2, uq.A9-2, and uq.C3-1, were identified. The transcriptomic results from extreme pools of DH lines with distinct seed vigor phenotypes during accelerated aging revealed that various biological pathways and metabolic processes (such as glutathione metabolism and reactive oxygen species) were involved in seed vigor. Through integration of QTL analysis and RNA-Seq, a regulatory network for the control of seed vigor was constructed. Importantly, a candidate (BnaOLE4) from cqSW-C2-3 was selected for functional analysis, and transgenic lines overexpressing BnaOLE4 showed increased seed vigor after artificial aging. Collectively, these results provide novel information on QTL and potential candidate genes for molecular breeding for improved seed storability.

Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice

BACKGROUND

Ongoing large-scale shift towards direct seeded rice (DSR) necessitates a convergence of breeding and genetic approaches for its sustenance and harnessing natural resources and environmental benefits. Improving seedling vigour remains key objective for breeders working with DSR. The present study aims to understand the genetic control of seedling vigour in deep sown DSR. Combined genome-wide association mapping, linkage mapping, fine mapping, RNA-sequencing to identify candidate genes and validation of putative candidate genes were performed in the present study.

RESULTS

Significant phenotypic variations were observed among genotypes in both F3:4:5 and BC2F2:3 populations. The mesocotyl length showed significant positive correlation with %germination, root and shoot length. The 881 kb region on chromosome 7 reported to be associated with mesocotyl elongation. RNA-seq data and RT-PCR results identified and validated seven potential candidate genes. The four promising introgression lines free from linkage drag and with longer mesocotyl length, longer root length, semi-dwarf plant height have been identified.

CONCLUSION

The study will provide rice breeders (1) the pre breeding material in the form of anticipated DSR adapted introgression lines possessing useful traits and alleles improving germination under deep sown DSR field conditions (2) the base for the studies involving functional characterization of candidate genes. The development and utilization of improved introgression lines and molecular markers may play an important role in genomics-assisted breeding (GAB) during the pyramiding of valuable genes providing adaptation to rice under DSR. Our results offer a robust and reliable package that can contribute towards enhancing genetic gains in direct seeded rice breeding programs.

Identification of a Seed Vigor-Related QTL Cluster Associated with Weed Competitive Ability in Direct-Seeded Rice (Oryza Sativa L.)

Direct seeding of rice (Oryza sativa L.) is a low-labor and sustainable cultivation method that is used worldwide. Seed vigor and early vigor are important traits associated with seedling stand density (SSD) and weed competitive ability (WCA), which are key factors in direct-seeded rice (DSR) cultivation systems. Here, we developed a set of chromosome segment substitution lines with Xiushui134 as receptor parent and Yangdao6 as donor parent and used these lines as a mapping population to identify quantitative trait loci (QTLs) for seed vigor, which we evaluated based on germinability-related indicators (germination percentage (GP), germination energy (GE), and germination index (GI)) and seedling vigor-related indicators (root number (RN), root length (RL), and shoot length (SL) at 14 days after imbibition) under controlled conditions in an incubator. Ten QTLs were detected across four chromosomes, of which a cluster of QTLs (qGP11, qGE11, qGI11, and qRL11) co-localized on Chr. 11 with high LOD values (12.03, 8.13, 7.14, and 8.75, respectively). Fine mapping narrowed down the QTL cluster to a 0.7-Mb interval between RM26797 and RM6680. Further analysis showed that the QTL cluster has a significant effect (p < 0.01) on early vigor under hydroponic culture (root length, total dry weight) and direct seeding conditions (tiller number, aboveground dry weight). Thus, our combined analysis revealed that the QTL cluster influenced both seed vigor and early vigor. Identifying favorable alleles at this QTL cluster could facilitate the improvement of SSD and WCA, thereby addressing both major factors in DSR cultivation systems.

Seasonal Variation in Cell Wall Composition and Carbohydrate Metabolism in the Seagrass Posidonia oceanica Growing at Different Depths

Posidonia oceanica is a common seagrass in the Mediterranean Sea that is able to sequester large amounts of carbon. The carbon assimilated during photosynthesis can be partitioned into non-structural sugars and cell-wall polymers. In this study, we investigated the distribution of carbon in starch, soluble carbohydrates and cell-wall polymers in leaves and rhizomes of P. oceanica. Analyses were performed during summer and winter in meadows located south of the Frioul archipelago near Marseille, France. The leaves and rhizomes were isolated from plants collected in shallow (2 m) and deep water (26 m). Our results showed that P. oceanica stores more carbon as starch, sucrose and cellulose in summer and that this is more pronounced in rhizomes from deep-water plants. In winter, the reduction in photoassimilates was correlated with a lower cellulose content, compensated with a greater lignin content, except in rhizomes from deep-water plants. The syringyl-to-guaiacyl (S/G) ratio in the lignin was higher in leaves than in rhizomes and decreased in rhizomes in winter, indicating a change in the distribution or structure of the lignin. These combined data show that deep-water plants store more carbon during summer, while in winter the shallow- and deep-water plants displayed a different cell wall composition reflecting their environment.

Novel QTL for Lateral Root Density and Length Improve Phosphorus Uptake in Rice (Oryza sativa L.)

The rice root system consists of two types of lateral roots, indeterminate larger L-types capable of further branching, and determinate, short, unbranched S-types. L-type laterals correspond to the typical lateral roots of cereals whereas S-type laterals are unique to rice. Both types contribute to nutrient and water uptake and genotypic variation for density and length of these laterals could be exploited in rice improvement to enhance adaptations to nutrient and water-limited environments. Our objectives were to determine how best to screen for lateral root density and length and to identify markers linked to genotypic variation for these traits. Using different growing media showed that screening in nutrient solution exposed genotypic variation for S-type and L-type density, but only the lateral roots of soil-grown plants varied for their lengths. A QTL mapping population developed from parents contrasting for lateral root traits was grown in a low-P field, roots were sampled, scanned and density and length of lateral roots measured. One QTL each was detected for L-type density (LDC), S-type density on crown root (SDC), S-type density on L-type (SDL), S-type length on L-type (SLL), and crown root number (RNO). The QTL for LDC on chromosome 5 had a major effect, accounting for 46% of the phenotypic variation. This strong positive effect was confirmed in additional field experiments, showing that lines with the donor parent allele at qLDC5 had 50% higher LDC. Investigating the contribution of lateral root traits to P uptake using stepwise regressions indicated LDC and RNO were most influential, followed by SDL. Simulating effects of root trait differences conferred by the main QTL in a P uptake model confirmed that qLDC5 was most effective in improving P uptake followed by qRNO9 for RNO and qSDL9 for S-type lateral density on L-type laterals. Pyramiding qLDC5 with qRNO9 and qSDL9 would be possible given that trade-offs between traits were not detected. Phenotypic selection for the RNO trait during variety development would be feasible, however, the costs of doing so reliably for lateral root density traits is prohibitive and markers identified here therefore provide the first opportunity to incorporate such traits into a breeding program.

Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations

Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were screened for mesocotyl length (ML) via dark germination. Six RDP1 accessions (Phudugey, Kasalath, CA902B21, Surjamkuhi, Djimoron, and Goria) had an ML longer than 10 cm, with the other 19 accessions being over 4 cm. A GWAS in RDP1 detected 118 associated SNPs on all 12 chromosomes using a threshold of FDR-adjusted p < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by -log₁₀(P) > 5.868 as the Bonferroni-corrected threshold. Using phenotypic data of three successive trials and a high-density bin map from resequencing genotypic data, four to six QTLs were detected on chromosomes 1, 2, 5, 6, and 10, including three loci repeatedly mapped for ML from two or three replicated trials. Candidate genes were predicted from the chromosomal regions covered by the associated LD blocks and the confidence intervals (CIs) of QTLs and partially validated by the dynamic RNA-seq data in the mesocotyl along different periods of light exposure. Potential strategies of donor parent selection for seedling establishment in DDSR breeding were discussed.

Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice

Seed vigor is the key performance parameter of good quality seed. A panel was prepared by shortlisting genotypes from all the phenotypic groups representing seedling growth parameters from a total of 278 germplasm lines. A wide variation was observed for the traits in the population. The panel was classified into four genetic structure groups. Fixation indices indicated the existence of linkage disequilibrium in the population. A moderate to high level of diversity parameters was assessed using 143 SSR markers. Principal component, coordinate, neighbor-joining tree and cluster analyses showed subpopulations with a fair degree of correspondence with the growth parameters. Marker-trait association analysis detected eight novel QTLs, namely qAGR4.1, qAGR6.1, qAGR6.2 and qAGR8.1 for absolute growth rate (AGR); qRSG6.1, qRSG7.1 and qRSG8.1 for relative shoot growth (RSG); and qRGR11.1 for relative growth rate (RGR), as analyzed by GLM and MLM. The reported QTL for germination rate (GR), qGR4-1, was validated in this population. Additionally, QTLs present on chromosome 6 controlling RSG and AGR at 221 cM and RSG and AGR on chromosome 8 at 27 cM were detected as genetic hotspots for the parameters. The QTLs identified in the study will be useful for improvement of the seed vigor trait in rice.

Physiological and genetic control of transpiration efficiency in African rice, Oryza glaberrima Steud

Improving crop water use efficiency, the amount of carbon assimilated as biomass per unit of water used by a plant, is of major importance as water for agriculture becomes scarcer. In rice, the genetic bases of transpiration efficiency, the derivation of water use efficiency at the whole-plant scale, and its putative component trait transpiration restriction under high evaporative demand remain unknown. These traits were measured in 2019 in a panel of 147 African rice (Oryza glaberrima) genotypes known to be potential sources of tolerance genes to biotic and abiotic stresses. Our results reveal that higher transpiration efficiency is associated with transpiration restriction in African rice. Detailed measurements in a subset of highly contrasted genotypes in terms of biomass accumulation and transpiration confirmed these associations and suggested that root to shoot ratio played an important role in transpiration restriction. Genome wide association studies identified marker-trait associations for transpiration response to evaporative demand, transpiration efficiency, and its residuals, with links to genes involved in water transport and cell wall patterning. Our data suggest that root-shoot partitioning is an important component of transpiration restriction that has a positive effect on transpiration efficiency in African rice. Both traits are heritable and define targets for breeding rice with improved water use strategies.

Meta-analysis of QTLs and candidate genes associated with seed germination in rice (Oryza sativa L.)

Seed germination is one of the critical stages of plant life, and many quantitative trait loci (QTLs) control this complex trait. Meta-analysis of QTLs is a powerful computational technique for estimating the most stable QTLs regardless of the population's genetic background. Besides, this analysis effectively narrows down the confidence interval (CI) to identify candidate genes (CGs) and marker development. In the current study, a comprehensive genome-wide meta-analysis was performed on QTLs associated with germination in rice. This analysis was conducted based on the data reported over the last two decades. In this case, various analyses were performed, including seed germination rate, plumule length, radicle length, germination percentage, coleoptile length, coleorhiza length, radicle fresh weight, germination potential, and germination index. A total of 67 QTLs were projected onto a reference map for these traits and then integrated into 32 meta-QTLs (MQTLs) to provide a genetic framework for seed germination. The average CI of MQTLs was considerably reduced from 15.125 to 8.73 cM compared to the initial QTLs. This situation identified 728 well-known functionally characterized genes and novel putative CGs for investigated traits. The fold change calculation demonstrated that 155 CGs had significant changes in expression analysis. In this case, 112 and 43 CGs were up-regulated and down-regulated during germination, respectively. This study provides an overview and compares genetic loci controlling traits related to seed germination in rice. The findings can bridge the gap between QTLs and CGs for seed germination.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01232-1.

The maize low-lignin brown midrib3 mutant shows pleiotropic effects on photosynthetic and cell wall metabolisms in response to chilling

Maize (Zea mays L.) is one of the major cereal crops in the world and is highly sensitive to low temperature. Here, changes in photosynthetic and cell wall metabolisms were investigated during a long chilling exposure in inbred line F2 and a low-lignin near-isogenic brown midrib3 mutant (F2bm3), which has a mutation in the caffeic acid O-methyltransferase (COMT) gene. Results revealed that the plant biomass was reduced, and this was more pronounced in F2bm3. Photosynthesis was altered in both lines with distinct changes in photosynthetic pigment content between F2bm3 and F2, indicating an alternative photoprotection mechanism between lines under chilling. Starch remobilization was observed in F2bm3 while concentrations of sucrose, fructose and starch increased in F2, suggesting a reduced sugar partitioning in F2. The cell wall was altered upon chilling, resulting in changes in the composition of glucuronorabinoxylan and a reduced cellulose level in F2. Chilling shifted lignin subunit composition in F2bm3 mutant to a higher proportion of p-hydroxyphenyl (H) units, whereas it resulted in lignin with a higher proportion of syringyl (S) residues in F2. On average, the total cell wall ferulic acid (FA) content increased in both genotypes, with an increase in ether-linked FA in F2bm3, suggesting a greater degree of cross-linking to lignin. The reinforcement of the cell wall with lignin enriched in H-units and a higher concentration in cell-wall-bound FA observed in F2bm3 as a response to chilling, could be a strategy to protect the photosystems.

Unraveling the genomic regions controlling the seed vigour index, root growth parameters and germination per cent in rice

High seed vigour ensures good quality seed and higher productivity. Early seedling growth parameters indicate seed vigour in rice. Seed vigour via physiological growth parameters is a complex trait controlled by many quantitative trait loci. A panel was prepared representing a population of 274 rice landraces by including genotypes from all the phenotypic groups of sixseedling stage physiological parameters including germination % for association mapping. Wide variations for the six studiedtraits were observed in the population. The population was classified into 3 genetic groups. Fixation indices indicated the presence of linkage disequilibrium in the population. The population was classified into subpopulations and each subpopulation showed correspondence with the 6 physiological traits. A total of 5 reported QTLs viz., qGP8.1 for germination % (GP); qSVII2.1, qSVII6.1 and qSVII6.2 for seed vigour index II (SVII), and qRSR11.1 for root-shoot ratio (RSR) were validated in this mapping population. In addition, 13 QTLs regulating the physiological parameters such as qSVI 11.1 for seed vigour index I; qSVI11.1 and qSVI12.1 for seed vigour index II; qRRG10.1, qRRG8.1, qRRG8.2, qRRG6.1 and qRRG4.1 for rate of root growth (RRG); qRSR2.1, qRSR3.1 and qRSR5.1 for root-shoot ratio (RSR) while qGP6.2 and qGP6.3 for germination %were identified. Additionally, co-localization or co-inheritance of QTLs, qGP8.1 and qSVI8.1 for GP and SVI-1; qGP6.2 and qRRG6.1 for GP and RRG, and qSVI11.1 and qRSR11.1 for SVI and RSR were detected. The QTLs identified in this study will be useful for improvement of seed vigour trait in rice.

Enhancement in Seed Priming-Induced Starch Degradation of Rice Seed Under Chilling Stress via GA-Mediated α-Amylase Expression

Chilling stress is the major abiotic stress that severely limited the seedling establishment of direct-seeded rice in temperate and sub-tropical rice production regions. While seed priming is an efficient pre-sowing seed treatment in enhancing crop establishment under abiotic stress. Our previous research has identified two seed priming treatments, selenium priming (Se) and salicylic priming (SA) that effectively improved the seed germination and seedling growth of rice under chilling stress. To further explore how seed priming enhance the starch degradation of rice seeds under chilling stress, the present study evaluated the effects of Se and SA priming on germination and seedling growth, α-amylase activity, total soluble sugar content, hormone content and associated gene relative expression under chilling stress. The results showed that both Se and SA priming significantly increased the seed germination and seedling growth attributes, and enhanced the starch degradation ability by increasing α-amylase activity and total soluble sugar content under chilling stress. Meanwhile, seed priming increased the transcription level of OsRamy1A, OsRamy3B that regulated by GA, and increased the transcription level of OsRamy3E that regulated by sugar signals. Furthermore, seed priming significantly improved the GA₃ contents in rice seeds by up-regulating the expression of OsGA3ox1 and OsGA20ox1, and decreased the ABA content and the expression of OsNCED1, indicating that the improved starch degradation ability in primed rice seeds under chilling stress might be attributed to the increased GA₃ and decreased ABA levels in primed rice seeds, which induced the expression of GA-mediated α-amylase. However, studies to explore how seed priming mediate hormonal metabolism and the expression of OsRamy3E are desperately needed.

The role of phytochrome-mediated gibberellic acid signaling in the modulation of seed germination under low light stress in rice (O. sativa L.)

Seed germination plays cardinal roles in seedling establishment and their successive growth. However, seed germination is retarded by far-red (FR) enrichment under low light stress, and the inhibitory signalling mechanism remains ambiguous. Our results indicated that low light treatment, both in the open and growth chamber conditions, inhibits rice seed germination by decreasing the gibberellin (GA) contents. To explore the mechanism of GA-deficiency under low light stress, differential expression profiling of GA-anabolic, -catabolic, ABA -anabolic, -catabolic, and SLR1 was investigated, revealing that expression of ABA- anabolic, GA-catabolic genes and SLR1 was upregulated with a simultaneous downregulation of ABA-catabolic and GA-anabolic genes under low light treatment. These results suggested that FR-induced GA inadequacy is resulted by upregulation of SLR1 and GA-catabolism genes consequently increase DELLA that further subsided GA-responses in the germinating rice seeds. Moreover, we provided evidence that FR-induced GA inadequacy demotes rice seed germination by decreasing amylase activity, eventually decreasing the carbohydrate solubilization in the germinating seeds. Finally, we suggest that under low light stress, due to a retarded conversion of phytochrome A to their bioactive form, the ABA-catabolic genes were eventually upregulated with a simultaneous downregulation of GA-anabolic genes. Consequently, a lower GA pool fails to leverage the GA-dependent DELLA degradation, further shutting down the expected GA responses that reduce germination efficiency under FR-enriched light.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01167-7.

Genome-wide association study reveals that the cupin domain protein OsCDP3.10 regulates seed vigour in rice

Seed vigour is an imperative trait for the direct seeding of rice. In this study, we examined the genetic regulation of seedling percentage at the early germination using a genome-wide association study in rice. One major quantitative trait loci qSP3 for seedling percentage was identified, and the candidate gene was validated as qSP3, encoding a cupin domain protein OsCDP3.10 for the synthesis of 52 kDa globulin. Disruption of this gene in Oscdp3.10 mutants reduced the seed vigour, including the germination potential and seedling percentage, at the early germination in rice. The lacking accumulation of 52 kDa globulin was observed in the mature grains of the Oscdp3.10 mutants. The significantly lower amino acid contents were observed in the mature grains and the early germinating seeds of the Oscdp3.10 mutants compared with those of wild-type. Rice OsCDP3.10 regulated seed vigour mainly via modulating the amino acids e.g. Met, Glu, His, and Tyr that contribute to hydrogen peroxide (H₂ O₂ ) accumulation in the germinating seeds. These results provide important insights into the application of seed priming with the amino acids and the selection of OsCDP3.10 to improve seed vigour in rice.

Analysis of gene expression in early seed germination of rice: landscape and genetic regulation

BACKGROUND

Seed germination is a crucial process, which determines the initiation of seed plant life cycle. The early events during this important life cycle transition that called early seed germination is defined as initially water uptake plus radicle growing out of the covering seed layers. However, a specific genome-wide analysis of early seed germination in rice is still obscure.

RESULTS

In this study, the physiological characteristics of rice seed during seed germination are determined to define key points of early seed germination. Transcriptome analyses of early phase of seed germination provided deeper insight into the genetic regulation landscape. Many genes involved in starch-to-sucrose transition were differentially expressed, especially alpha-amylase 1b and beta-amylase 2, which were predominantly expressed. Differential exon usage (DEU) genes were identified, which were significantly enriched in the pathway of starch and sucrose metabolism, indicating that DEU events were critical for starch-to-sucrose transition at early seed germination. Transcription factors (TFs) were also dramatic expressed, including the abscisic acid (ABA) responsive gene, OsABI5, and gibberellic acid (GA) responsive genes, GAI. Moreover, GAI transactivated GA responsive gene, GAMYB in vivo, indicating a potential pathway involved in early seed germination process. In addition, CBL-interacting protein kinase (CIPK) genes, such as CIPK13, CIPK14 and CIPK17 were potentially interacted with other proteins, indicating its pivotal role at early seed germination.

CONCLUSION

Taken together, gene regulation of early seed germination in rice was complex and protein-to-gene or protein-to-protein interactions were indispensable.

A Genome Wide Association Study Revealed Key Single Nucleotide Polymorphisms/Genes Associated With Seed Germination in Gossypium hirsutum L

Fast and uniform seed germination is essential to stabilize crop yields in agricultural production. It is important to understand the genetic basis of seed germination for improving the vigor of crop seeds. However, little is known about the genetic basis of seed vigor in cotton. In this study, we evaluated four seed germination-related traits of a core collection consisting of 419 cotton accessions, and performed a genome-wide association study (GWAS) to explore important loci associated with seed vigor using 3.66 million high-quality single nucleotide polymorphisms (SNPs). The results showed that four traits, including germination potential, germination rate, germination index, and vigor index, exhibited broad variations and high correlations. A total of 92 significantly associated SNPs located within or near 723 genes were identified for these traits, of which 13 SNPs could be detected in multiple traits. Among these candidate genes, 294 genes were expressed at seed germination stage. Further function validation of the two genes of higher expression showed that Gh_A11G0176 encoding Hsp70-Hsp90 organizing protein negatively regulated Arabidopsis seed germination, while Gh_A09G1509 encoding glutathione transferase played a positive role in regulating tobacco seed germination and seedling growth. Furthermore, Gh_A09G1509 might promote seed germination and seedling establishment through regulating glutathione metabolism in the imbibitional seeds. Our findings provide unprecedented information for deciphering the genetic basis of seed germination and performing molecular breeding to improve field emergence through genomic selection in cotton.

Primary Root and Mesocotyl Elongation in Maize Seedlings: Two Organs with Antagonistic Growth below the Soil Surface

Maize illustrates one of the most complex cases of embryogenesis in higher plants that results in the development of early embryo with distinctive organs such as the mesocotyl, seminal and primary roots, coleoptile, and plumule. After seed germination, the elongation of root and mesocotyl follows opposite directions in response to specific tropisms (positive and negative gravitropism and hydrotropism). Tropisms represent the differential growth of an organ directed toward several stimuli. Although the life cycle of roots and mesocotyl takes place in darkness, their growth and functions are controlled by different mechanisms. Roots ramify through the soil following the direction of the gravity vector, spreading their tips into new territories looking for water; when water availability is low, the root hydrotropic response is triggered toward the zone with higher moisture. Nonetheless, there is a high range of hydrotropic curvatures (angles) in maize. The processes that control root hydrotropism and mesocotyl elongation remain unclear; however, they are influenced by genetic and environmental cues to guide their growth for optimizing early seedling vigor. Roots and mesocotyls are crucial for the establishment, growth, and development of the plant since both help to forage water in the soil. Mesocotyl elongation is associated with an ancient agriculture practice known as deep planting. This tradition takes advantage of residual soil humidity and continues to be used in semiarid regions of Mexico and USA. Due to the genetic diversity of maize, some lines have developed long mesocotyls capable of deep planting while others are unable to do it. Hence, the genetic and phenetic interaction of maize lines with a robust hydrotropic response and higher mesocotyl elongation in response to water scarcity in time of global heating might be used for developing more resilient maize plants.

Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture

The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.

Identification and fine mapping of qGR6.2, a novel locus controlling rice seed germination under salt stress

BACKGROUND

Rice growth is frequently affected by salinity. When exposed to high salinity, rice seed germination and seedling establishment are significantly inhibited. With the promotion of direct-seeding in Asia, improving rice seed germination under salt stress is crucial for breeding.

RESULTS

In this study, an indica landrace Wujiaozhan (WJZ) was identified with high germinability under salt stress. A BC₁F₂ population derived from the crossing WJZ/Nip (japonica, Nipponbare)//Nip, was used to quantitative trait loci (QTL) mapping for the seed germination rate (GR) and germination index (GI) under H₂O and 300 mM NaCl conditions. A total of 13 QTLs were identified, i.e. ten QTLs under H₂O conditions and nine QTLs under salt conditions. Six QTLs, qGR6.1, qGR8.1, qGR8.2, qGR10.1, qGR10.2 and qGI10.1 were simultaneously identified under two conditions. Under salt conditions, three QTLs, qGR6.2, qGR10.1 and qGR10.2 for GR were identified at different time points during seed germination, which shared the same chromosomal region with qGI6.2, qGI10.1 and qGI10.2 for GI respectively. The qGR6.2 accounted for more than 20% of phenotypic variation under salt stress, as the major effective QTL. Furthermore, qGR6.2 was verified via the BC₂F₂ population and narrowed to a 65.9-kb region with eleven candidate genes predicted. Based on the microarray database, five candidate genes were found with high transcript abundances at the seed germination stage, of which LOC_Os06g10650 and LOC_Os06g10710 were differentially expressed after seed imbibition. RT-qPCR results showed the expression of LOC_Os06g10650 was significantly up-regulated in two parents with higher levels in WJZ than Nip during seed germination under salt conditions. Taken together, it suggests that LOC_Os06g10650, encoding tyrosine phosphatase family protein, might be the causal candidate gene for qGR6.2.

CONCLUSIONS

In this study, we identified 13 QTLs from a landrace WJZ that confer seed germination traits under H₂O and salt conditions. A major salt-tolerance-specific QTL qGR6.2 was fine mapped to a 65.9-kb region. Our results provide information on the genetic basis of improving rice seed germination under salt stress by marker-assisted selection (MAS).

Mapping QTL hotspots associated with weed competitive traits in backcross population derived from Oryza sativa L. and O. glaberrima Steud

To improve grain yield under direct seeded and aerobic conditions, weed competitive ability of a rice genotype is a key desirable trait. Hence, understanding and dissecting weed competitive associated traits at both morphological and molecular level is important in developing weed competitive varieties. In the present investigation, the QTLs associated with weed competitive traits were identified in BC1F2:3 population derived from weed competitive accession of O. glaberrima (IRGC105187) and O. sativa cultivar IR64. The mapping population consisting of 144 segregating lines were phenotyped for 33 weed competitive associated traits under direct seeded condition. Genetic analysis of weed competitive traits carried out in BC1F2:3 population showed significant variation for the weed competitive traits and predominance of additive gene action. The population was genotyped with 81 genome wide SSR markers and a linkage map covering 1423 cM was constructed. Composite interval mapping analysis identified 72 QTLs linked to 33 weed competitive traits which were spread on the 11 chromosomes. Among 72 QTLs, 59 were found to be major QTLs (> 10% PVE). Of the 59 major QTLs, 38 had favourable allele contributed from the O. glaberrima parent. We also observed nine QTL hotspots for weed competitive traits (qWCA2a, qWCA2b, qWCA2c, qWCA3, qWCA5, qWCA7, qWCA8, qWCA9, and qWCA10) wherein several QTLs co-localised. Our study demonstrates O. glaberrima species as potential source for improvement for weed competitive traits in rice and identified QTLs hotspots associated with weed competitive traits.

Genetic analysis of rice seedling traits related to machine transplanting under different seeding densities

BACKGROUND

Due to the diversity of rice varieties and cropping systems in China, the limitation of seeding density and seedling quality makes it hard to improve machine-transplanted efficiency. Previous studies have shown that indica and japonica varieties varied in machine transplanting efficiency and optimal seeding density. In this study, a RIL population derived from '9311' and 'Nipponbare' were performed to explore the seedling traits variations and the genetic mechanism under three seeding densities.

RESULTS

The parents and RIL population exhibited similar trends as the seeding density increased, including seedling height and first leaf sheath length increases, shoot dry weight and root dry weight decreases. Among the 37 QTLs for six traits detected under the three seeding densities, 12 QTLs were detected in both three seeding densities. Five QTL hotspots identified clustered within genomic regions on chromosomes 1, 2, 4, 6 and 11. Specific QTLs such as qRDW_1.1 and qFLSL_5.1 were detected under low and high seeding densities, respectively. Detailed analysis the QTL regions identified under specific seeding densities revealed several candidate genes involved in phytohormones signals and abiotic stress responses. Whole-genome additive effects showed that '9311' contributed more loci enhancing trait performances than 'Nipponbare', indicating '9311' was more sensitive to the seeding density than 'Nipponbare'. The prevalence of negative epistasis effects indicated that the complementary two-locus homozygotes may not have marginal advantages over the means of the two parental genotypes.

CONCLUSIONS

Our results revealed the differences between indica rice and japonica rice seedling traits in response to seeding density. Several QTL hotspots involved in different traits and specific QTLs (such as qRDW_1.1 and qFLSL_5.1) in diverse seeding densities had been detected. Genome-wide additive and two-locus epistasis suggested a dynamic of the genetic control underlying different seeding densities. It was concluded that novel QTLs, additive and epistasis effects under specific seeding density would provide adequate information for rice seedling improvement during machine transplanting.

Association of molecular markers with physio-biochemical traits related to seed vigour in rice

Eighteen physio-biochemical traits influencing seed vigour were studied for their association with molecular markers using a mini core set constituted from 120 germplasm lines. High genetic variation was detected in the parameters namely chlrophyll a, Chlrophyll b, total chlorophyll, carotenoids, total anthocyanin content, gamma-oryzanols, total phenolics content, superoxide dismutase, catalase, guaicol peroxidase, total soluble sugar, total protein, seed vigour index -I and seed vigour index -II. Strong positive correlation of seed vigour index II was observed with amylose content, total anthocyanin content, catalase, total phenolic content and total flavonoid content while a negative association was observed for gamma-oryzanol content. High gene diversity (0.7169) and informative markers value (0.6789) were estimated from the investigation. Three genetic structure groups were observed in the panel population and genotypes were grouped in the subpopulations based on the seed vigour trait. Differences in the fixation indices of the three sub populations indicated existence of linkage disequilibrium in the studied panel population. Association of the traits namely total flavonoids, superoxide dismutase, catalase, chlorophyll a, Chlorophyll b, total chlorophyll, carotenoids, starch, amylose, total anthocyanin, gamma-oryzanol, total phenolics with the molecular markers were detected by Generalized Linear Model and Mixed Linear Model showing > 0.10 R² value. Association of the trait, total flavonoids with marker RM7364 located on chromosome 8 reported in earlier study was validated in this investigation. The validated markers and the novel markers detected showing higher R² value will be useful for improvement of seed vigour in rice.

Cruz PC, Baltazar AM, Diaz MGQ, Pang YL, Acero BL, Li Z. Identification of quantitative trait loci governing early germination and seedling vigor traits related to weed competitive ability in rice

Weed competitive ability (WCA) is vital for the improvement of grain yield under direct-seeded and aerobic rice ecosystems where weeds are a major limiting factor. Early seed germination (ESG) and early seedling vigor (ESV) are the crucial traits for WCA. This study attempted to map the quantitative trait loci (QTLs) and hotspot regions governing ESG and ESV traits. A total of 167 BC1F5 selective introgression lines developed from an early backcross population involving Weed Tolerant Rice 1 (WTR-1) as the recipient parent and Y-134 as the donor parent were phenotyped for ESG and ESV traits. Analysis of variance revealed significant differences in ESG-related traits except for root length and in ESV-related traits except for plant height at 7 days after sowing. A total of 677-high quality single nucleotide polymorphism (SNP) markers were used to analyze the marker-trait association from a 6 K SNP genotyping array. Forty-three QTLs were identified on all chromosomes, except on chromosomes 4 and 8. Thirty QTLs were contributed by a desirable allele from Y-134, whereas 13 QTLs were from WTR-1. Twenty-eight of the identified genetic loci associated with ESG and ESV traits were novel. Two QTL hotspot regions were mapped on chromosomes 11 and 12. The genomic regions of QTL hotspots were fine-tuned and a total of 13 putative candidate genes were discovered on chromosomes 11 and 12 collectively. The mapped QTLs will be useful in advancing the marker aided-selection schemes and breeding programs for the development of rice cultivars with WCA traits.

Morphological and physiological factors contributing to early vigor in the elite rice cultivar 9,311

Huanghuazhan (HHZ) and 9,311 are two elite rice cultivars in China. They have achieved high yield through quite different mechanisms. One of the major features that gives high yield capacity to 9,311 is its strong early vigor, i.e., faster establishment of its seedling as well as its better growth in its early stages. To understand the mechanistic basis of early vigor in 9,311, as compared to HHZ the cultivar, we have examined, under controlled environmental conditions, different morphological and physiological traits that may contribute to its early vigor. Our results show that the fresh weight of the seeds, at germination, not only determined the seedling biomass at 10 days after germination (DAG), but was also responsible for ~ 80% of variations in plant biomass between the two cultivars even up to 30 DAG. Furthermore, the 9,311 cultivar had a larger root system, which led to its higher nitrogen uptake capacity. Other noteworthy observations about 9,311 being a better cultivar than HHZ are: (i) Ten out of 15 genes involved in nitrogen metabolism were much more highly expressed in its roots; (ii) it had a higher water uptake rate, promoting better root-to-shoot nitrogen transfer; and (iii) consistent with the above, it had higher leaf photosynthetic rate and stomatal conductance. All of the above identified features explain, to a large extent, why the 9,311, as compared to HHZ, exhibits much more vigorous early growth.

Genome-Wide Association Mapping to Identify Genetic Loci for Cold Tolerance and Cold Recovery During Germination in Rice

Low temperature significantly affects rice growth and yield. Temperatures lower than 15°C are generally detrimental for germination and uniform seedling stand. To investigate the genetic architecture underlying cold tolerance during germination in rice, we conducted a genome-wide association study using a novel diversity panel of 257 rice accessions from around the world and the 7K SNP marker array. Phenotyping was conducted in controlled growth chambers under dark conditions at 13°C. The rice accessions were measured for low-temperature germinability, germination index, coleoptile length under cold stress, plumule length at 4-day recovery, and plumule length recovery rate. A total of 51 QTLs were identified at p < 0.001 and 17 QTLs were identified using an FDR < 0.05 across the different chilling indices with the whole panel of accessions. At the threshold of p < 0.001, a total of 20 QTLs were identified in the subset of japonica accessions, while 9 QTLs were identified in the subset of indica accessions. Considering the recurring SNPs and linked SNPs across different chilling indices, we identified 31 distinct QTL regions in the whole panel, 13 QTL regions in the japonica subset, and 7 distinct QTL regions in the indica subset. Among these QTL regions, three regions were common between the whole panel and japonica, three regions were common between the whole panel and indica, and one region was common between indica and japonica. A subset of QTL regions was potentially colocalized with previously identified genes and QTLs, including 10 from the japonica subset, 4 from the indica subset, and 6 from the whole panel. On the other hand, a total of 21 potentially novel QTL regions from the whole panel, 10 from the japonica subset, and 1 from the indica subset were identified. The results of our study provide useful information on the genetic architecture underlying cold tolerance during germination in rice, which in turn can be used for further molecular study and crop improvement for low-temperature stressed environments.

Identification of Quantitative Trait Loci Controlling Ethylene Production in Germinating Seeds in Maize (Zea mays L.)

Plant seed germination is a crucial developmental event that has significant effects on seedling establishment and yield production. This process is controlled by multiple intrinsic signals, particularly phytohormones. The gaseous hormone ethylene stimulates seed germination; however, the genetic basis of ethylene production in maize during seed germination remains poorly understood. In this study, we quantified the diversity of germination among 14 inbred lines representing the parental materials corresponding to multiple recombinant inbred line (RIL) mapping populations. Quantitative trait loci (QTLs) controlling ethylene production were then identified in germinating seeds from an RIL population constructed from two parental lines showing differences in both germination speed and ethylene production during germination. To explore the possible genetic correlations of ethylene production with other traits, seed germination and seed weight were evaluated using the same batch of samples. On the basis of high-density single nucleotide polymorphism-based genetic linkage maps, we detected three QTLs for ethylene production in germinating seeds, three QTLs for seed germination, and four QTLs for seed weight, with each QTL explaining 5.8%–13.2% of the phenotypic variation of the trait. No QTLs were observed to be co-localized, suggesting that the genetic bases underlying the three traits are largely different. Our findings reveal three chromosomal regions responsible for ethylene production during seed germination, and provide a valuable reference for the future investigation of the genetic mechanism underlying the role of the stress hormone ethylene in maize germination control under unfavourable external conditions.

Mining of favorable alleles for seed reserve utilization efficiency in Oryza sativa by means of association mapping

Background

Wet direct-seeded rice is a possible alternative to conventional puddled transplanted rice; the former uses less water and reduces labor requirements. Improving seed reserve utilization efficiency (SRUE) is a key factor in facilitating the application of this technology. However, the QTLs controlling this trait are poorly investigated. In this study, a genome-wide association study (GWAS) was conducted using a natural population composed of 542 accessions of rice (Oryza sativa L.) which were genotyped using 266 SSR markers. Large phenotypic variations in SRUE were found in the studied population.

Results

The average SRUE over 542 accessions across two years (2016 and 2017) was 0.52 mg.mg^− 1, ranging from 0.22 mg.mg-¹ to 0.93 mg.mg^− 1, with a coefficient of variation of 22.66%. Overall, 2879 marker alleles were detected in the population by 266 pairs of SSR markers, indicating a large genetic variation existing in the population. Using general linear model method, 13 SSR marker loci associated with SRUE were detected and two (RM7309 and RM434) of the 13 loci, were also detected using mixed linear model analyses, with percentage of phenotypic variation explained (PVE) greater than 5% across two years. The 13 association loci (P < 0.01) were located on all chromosomes except chromosome 11, with PVE ranging from 5.05% (RM5158 on chromosome 5) to 12% (RM297 on chromosome 1). Association loci RM7309 on chromosome 6 and RM434 on chromosome 9 revealed by both models were detected in both years. Twenty-three favorable alleles were identified with phenotypic effect values (PEV) ranging from 0.10 mg.mg^− 1 (RM7309–135 bp on chromosome 9) to 0.45 mg.mg^− 1 (RM297–180 bp on chromosome 2). RM297–180 bp showed the largest phenotypic effect value (0.44 mg.mg^− 1 in 2016 and 0.45 mg.mg^− 1 in 2017) with 6.72% of the accessions carrying this allele and the typical carrier accession was Manyedao, followed by RM297–175 bp (0.43 mg.mg^− 1 in 2016 and 0.44 mg.mg^− 1 in 2017).

Conclusion

Nine novel association loci for SRUE were identified, compared with previous studies. The optimal parental combinations for pyramiding more favorable alleles for SRUE were selected and could be used for breeding rice accessions suitable for wet direct seeding in the future.

New Parameters for Seedling Vigor Developed via Phenomics

Early seedling establishment in rice (Oryza sativa L.), which is measured by primary/secondary tiller, shoot length, biomass, root-related traits, and leaf area index, is an important trait because it helps to compete for light, air, and water for better tolerating various abiotic stresses. Consequently, it can affect the yield. However, there are not many research studies on this subject. Furthermore, previous studies have only measured the target traits once. However, this does not reflect the variation of growth rate during the seedling stage. Thus, two data points, two weeks and four weeks after planting, were used in the current study. As a result, two QTL regions were detected for the growth differences via plant height and green area (reflecting tillering). We expect that these results can be utilized by breeders to evaluate and select vigorous seedlings for their breeding programs.

Genetic dissection of seedling vigour in a diverse panel from the 3,000 Rice (Oryza sativa L.) Genome Project

Seedling vigour (SV) is important for direct seeding rice (Oryza sativa L.), especially in a paddy-direct seeding system, but the genetic mechanisms behind the related traits remain largely unknown. Here, we used 744 germplasms, having at least two subsets, for the detection of quantitative trait loci (QTLs) affecting the SV-related traits tiller number, plant height, and aboveground dry weight at three sampling stages, 27, 34, and 41 d after sowing. A joint map based on GAPIT and mrMLM produced a satisfying balance between type I and II errors. In total, 42 QTL regions, containing 18 (42.9%) previously reported overlapping QTL regions and 24 new ones, responsible for SV were detected throughout the genome. Four QTL regions, qSV1a, qSV3e, qSV4c, and qSV7c, were delimited and harboured quantitative trait nucleotides that are responsible for SV-related traits. Favourable haplotype mining for the candidate genes within these four regions, as well as the early SV gene OsGA20ox1, was performed, and the favourable haplotypes were presented with donors from the 3,000 Rice Genome Project. This work provides new information and materials for the future molecular breeding of direct seeding rice, especially in paddy-direct seeding cultivation systems.

Quantitative Trait Locus Analysis of Seed Germination and Early Seedling Growth in Rice

Seed germination and early seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice (DSR). To investigate the genetic mechanisms underlying seed germination and early seedling growth in rice, 275 recombinant inbred lines (RILs) were genotyped in this study via the genotyping-by-sequencing (GBS) approach to construct a high-density linkage bin map based on the parent-independent genotyping method. Quantitative trait loci (QTLs) for 12 traits related to seed germination and early seedling growth were analyzed. Totally, 22 additive loci were detected, after analysis of the interaction between additive QTLs and environments, five stable additive loci were obtained. Among them, loci 4, 5, 12 and 14 exhibited clear pleiotropic effects that were associated with multiple traits. Analysis of the effects of the five additive stable loci showed that a single locus increased the corresponding phenotypic value. Ten of the 275 RILs pyramided the excellent alleles of the five stable genetic loci. Most phenotypic values of the ten RILs were greater than the average values. Four RILs (G260, G342, G371, and G401) with more excellent phenotypic values were subsequently selected; these RILs could serve as donor parents of favorable alleles in the breeding process. Due to the existence of pleiotropy, the use of these genetic loci for pyramid breeding can further increase the efficiency to reach breeding goals. In addition, these five stable loci have an average physical interval of only 170 kb, we also further identified five promising candidate genes by qRT-PCR, which provides us with a basis for future cloning of these genes. Overall, this work will help broaden our understanding of the genetic control of seed germination and early seedling growth, and this study provides both a good theoretical basis and a new genetic resource for the breeding of direct-seeded rice.

Genome-wide association and gene validation studies for early root vigour to improve direct seeding of rice

Elucidation of the genetic control of rice seedling vigour is now paramount with global shifts towards direct seeding of rice and the consequent demand for early vigour traits in breeding programmes. In a genome-wide association study using an indica-predominant diversity panel, we identified quantitative trait loci (QTLs) for root length and root number in rice seedlings. Among the identified QTLs, one QTL for lateral root number on chromosome 11, qTIPS-11, was associated with a 32.4% increase in lateral root number. The locus was validated in independent backgrounds, and a predicted glycosyl hydrolase, TIPS-11-9, was identified as the causal gene for observed phenotypic differences. TIPS-11-9 was differentially expressed in emerging lateral roots of contrasting qTIPS-11 haplotypes, which was likely due to differences in cis-regulatory elements and auxin responsiveness. Abolishment of Tips-11-9 function through T-DNA insertion in a qTIPS-11-positive background resulted in a reduction of lateral root number, which negatively affected biomass accumulation, particularly under phosphorous-limiting conditions. Marker-assisted introgression of qTIPS-11 into modern indica varieties will aid in the generation of varieties adapted to direct seeding and thus facilitate the adoption of direct seeding practices in tropical Asia.

Rhizobia promote the growth of rice shoots by targeting cell signaling, division and expansion

The growth-promotion of rice seedling following inoculation with Sinorhizobium meliloti 1021 was a cumulative outcome of elevated expression of genes that function in accelerating cell division and enhancing cell expansion. Various endophytic rhizobacteria promote the growth of cereal crops. To achieve a better understanding of the cellular and molecular bases of beneficial cereal-rhizobia interactions, we performed computer-assisted microscopy and transcriptomic analyses of rice seedling shoots (Oryza sativa) during early stages of endophytic colonization by the plant growth-promoting Sinorhizobium meliloti 1021. Phenotypic analyses revealed that plants inoculated with live rhizobia had increased shoot height and dry weight compared to control plants inoculated with heat-killed cells of the same microbe. At 6 days after inoculation (DAI) with live cells, the fourth-leaf sheaths showed significant cytological differences including their enlargement of parenchyma cells and reduction in shape complexity. Transcriptomic analysis of shoots identified 2,414 differentially-expressed genes (DEGs) at 1, 2, 5 and 8 DAI: 195, 1390, 1025 and 533, respectively. Among these, 46 DEGs encoding cell-cycle functions were up-regulated at least 3 days before the rhizobia ascended from the roots to the shoots, suggesting that rhizobia are engaged in long-distance signaling events during early stages of this plant-microbe interaction. DEGs involved in phytohormone production, photosynthetic efficiency, carbohydrate metabolism, cell division and wall expansion were significantly elevated at 5 and 8 DAI, consistent with the observed phenotypic changes in rice cell morphology and shoot growth-promotion. Correlation analysis identified 104 height-related DEGs and 120 dry-weight-related DEGs that represent known quantitative-trait loci for seedling vigor and increased plant height. These findings provide multiple evidences of plant-microbe interplay that give insight into the growth-promotion processes associated with this rhizobia-rice beneficial association.

Magnesium and organic biostimulant integrative application induces physiological and biochemical changes in sunflower plants and its harvested progeny on sandy soil

Magnesium (Mg) often leaches down in sandy soils due to high mobility and its foliar application proves to be beneficial. Organic biostimulants also prove to be helpful to affect plant physio-biochemistry and antioxidative defense system. The present study evaluated the beneficial effects of seed soaking in maize grain extract (MGE; 3%) in integration with or without foliar Mg (1 mM) in comparison to control (no treatment) on growth, yield performance, seed oil and fatty acid profile including physiological and biochemical basis of Hysun-336 sunflower hybrid grown on a sandy soil under greenhouse conditions. The integrative treatment (seed soaking in MGE + foliar spray with Mg) elevated growth traits, plant water status and membrane stability index, and reduced electrolyte leakage. Improved leaf contents of chlorophylls, carotenoids, total soluble sugars and proline, activities of non-enzymatic and enzymatic antioxidants were also observed. In addition, enhanced uptake of N, P, K including Mg and endogenous levels of plant hormones IAA, GA₃ and zeatin were recorded with the integrative treatment. Seed yield and oil contents including oleic (mono-unsaturated) and linoleic (poly-unsaturated) fatty acids also increased; however, a decrease in other saturated, mono-unsaturated and poly-unsaturated fatty acids was noticed. Improved seed and seedling vigor traits were also observed in progeny of sunflower that harvested from the integrative treatment. In summary, improved plant performance by the integrative treatment may be attributed to improved activities of antioxidants contributing to improved plant water content, nutrient uptake and endogenous hormonal levels in sunflower plants grown under sandy soil conditions.

Genome-wide association study reveals candidate genes related to low temperature tolerance in rice (Oryza sativa) during germination

In this study, relative germination percentage (RGP) and delayed mean germination time (DMGT) were measured in various rice accessions at the germination stage and carried out association analysis to identify candidate genes related to low temperature germination (LTG) using a natural population comprising 137 rice cultivars and inbred lines selected from the Korean rice core set. Genome-wide association study using ~ 1.44 million high-quality SNPs, which were identified by re-sequencing all rice collections, revealed 48 candidate genes on chromosome 10 and 55 candidate genes on chromosome 11 in the high peak SNP sites of associated loci for RGP and DMGT, respectively. By detecting highly associated variations located inside genic regions and performing functional annotation of the genes, we detected 23 candidate genes for RGP and 18 genes for DMGT for LTG. In addition, the haplotype and sequence analysis of the candidate gene (Os10g0371100) with RGP trait and the candidate gene (Os11t0104240-00) with DMGT revealed correlation between sequences of functional variations and phenotypes. Several novel LTG-related candidate genes previously were known for the function during rice germination and uncovered their substantial natural variations. These candidate genes represent valuable resources for molecular breeding and genetic improvement of cold tolerance during rice germination.

Shanyou 63: an elite mega rice hybrid in China

Hybrid rice has been successfully used for commercial rice production for 40 years in China. Shanyou 63, a mega rice hybrid, derived from the parents Zhenshan 97A and Minghui 63, was a milestone for China's hybrid rice development and production because of its high yield and wide adaptability. It was planted in 16 provinces of the country on 17% of the national hybrid rice area annually during the 29 years from 1984 to 2012. The hybrid and its parents have also been widely used for basic and agronomic studies related to rice heterosis, stress tolerance, molecular markers and genomics. We review the development of the hybrid and its parents and their major characteristics for the purpose of learning from the history and guiding future hybrid rice development. The history and development experience show that a successful hybrid rice variety should have multiple traits, including high yield, wide adaptability, resistances to major diseases, and high rice quality that meets the demands of consumers. From the breeding aspect, hybrid rice provides the advantage of combining elite traits or genes from different types of parents, such as those from subspecies of indica and japonica, into a single variety. Farmers prefer not only a variety with high yield potential, but also stable yields and local adaptability.

Rapid evaluation of seed vigor by the absolute content of protein in seed within the same crop

Seed vigor, an important index of seed quality, determines the potential for rapid and uniform emergence of plants. The objective of this study was to explore a rapid method for evaluating seed vigor. To analyze the correlation of seed traits and seedling traits related to seed vigor, we designed five experiments including nitrogen fertilizer, irrigation and seed sorting treatments in wheat. The results showed that only the absolute content of protein (ACP) in wheat seed was significantly correlated with plant dry weight in five experiments. Subsequently, another experiment including 30 wheat seed lots was used to validate the above results. Although 100-grain weight was also correlated with plant dry weight (R = 0.799, p < 0.01), the correlation coefficient was lower than that between ACP in seed and plant dry weight (R = 0.897, p < 0.01). Moreover, the results of three experiments using maize seeds was similar with above. The relative content of protein in seed detected by near-infrared spectrum combining with seed weight could realize rapid and nondestructive testing ACP in seed. Collectively, ACP in crop seed could be applied in rapid evaluation of seed vigor and could potentially be used for processing and screening high vigor seeds.

Regulation of Seed Vigor by Manipulation of Raffinose Family Oligosaccharides in Maize and Arabidopsis thaliana

Raffinose family oligosaccharides (RFOs) accumulate in seeds during maturation desiccation in many plant species. However, it remains unclear whether RFOs have a role in establishing seed vigor. GALACTINOL SYNTHASE (GOLS), RAFFINOSE SYNTHASE (RS), and STACHYOSE SYNTHASE (STS) are the enzymes responsible for RFO biosynthesis in plants. Interestingly, only raffinose is detected in maize seeds, and a unique maize RS gene (ZmRS) was identified. In this study, we found that two independent mutator (Mu)-interrupted zmrs lines, containing no raffinose but hyperaccumulating galactinol, have significantly reduced seed vigor, compared with null segregant controls. Unlike maize, Arabidopsis thaliana seeds contain several RFOs (raffinose, stachyose, and verbascose). Manipulation of A. thaliana RFO content by overexpressing ZmGOLS2, ZmRS, or AtSTS demonstrated that co-overexpression of ZmGOLS2 and ZmRS, or overexpression of ZmGOLS2 alone, significantly increased the total content of RFOs and enhanced Arabidopsis seed vigor. Surprisingly, while overexpression of ZmRS increased seed raffinose content, its overexpression dramatically decreased seed vigor and reduced the seed amounts of galactinol, stachyose, and verbascose. In contrast, the atrs5 mutant seeds are similar to those of the wild type with regard to seed vigor and RFO content, except for stachyose, which accumulated in atrs5 seeds. Total RFOs, RFO/sucrose ratio, but not absolute individual RFO amounts, positively correlated with A. thaliana seed vigor, to which stachyose and verbascose contribute more than raffinose. Taken together, these results provide new insights into regulatory mechanisms of seed vigor and reveal distinct requirement for RFOs in modulating seed vigor in a monocot and a dicot.

Genome-wide association study of salt tolerance at the seed germination stage in rice

BACKGROUND

Improving the salt tolerance of direct-seeding rice at the seed germination stage is a major breeding goal in many Asian rice-growing countries, where seedlings must often establish in soils with a high salt content. Thus, it is important to understand the genetic mechanisms of salt tolerance in rice and to screen for germplasm with salt tolerance at the seed germination stage. Here, we investigated seven seed germination-related traits under control and salt-stress conditions and conducted a genome-wide association study based on the re-sequencing of 478 diverse rice accessions.

RESULTS

The analysis used a mixed linear model and was based on 6,361,920 single nucleotide polymorphisms in 478 rice accessions grouped into whole, indica, and non-indica panels. Eleven loci containing 22 significant salt tolerance-associated single nucleotide polymorphisms were identified based on the stress-susceptibility indices (SSIs) of vigor index (VI) and mean germination time (MGT). From the SSI of VI, six major loci were identified, explaining 20.2% of the phenotypic variation. From the SSI of MGT, five major loci were detected, explaining 26.4% of the phenotypic variation. Of these, seven loci on chromosomes 1, 5, 6, 11, and 12 were close to six previously identified quantitative gene loci/genes related to tolerance to salinity or other abiotic stresses. The strongest association region for the SSI of MGT was identified in a ~ 13.3 kb interval (15450039-15,463,330) on chromosome 1, near salt-tolerance quantitative trait loci controlling the Na⁺: K⁺ ratio, total Na⁺ uptake, and total K⁺ concentration. The strongest association region for the SSI of VI was detected in a ~ 164.2 kb interval (526662-690,854) on chromosome 2 harboring two nitrate transporter family genes (OsNRT2.1 and OsNRT2.2), which affect gene expression under salt stress. The haplotype analysis indicated that OsNRT2.2 was associated with subpopulation differentiation and its minor/rare tolerant haplotype was detected.

CONCLUSIONS

These results provide valuable information for salt tolerance-related gene cloning and for understanding the genetic mechanisms of salt tolerance at the seed germination stage. This information will be useful to improve the salt tolerance of direct-seeding rice varieties by genomic selection or marker-assisted selection.

Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis

Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA accessions.

QTL Hotspots for Early Vigor and Related Traits under Dry Direct-Seeded System in Rice (Oryza sativa L.)

Strong seedling vigor is desirable trait in dry direct-seeded rice (DSR) for enhancing crop establishment and the ability to compete against weeds. A set of 253 BC3F4 lines derived from cross between Swarna and Moroberekan was phenotyped for early vigor (EV) and 8 related traits viz., early uniform emergence (EUE), shoot length (SHL), stem length (SL), shoot fresh weight (SFW), total fresh weight (TFW), shoot dry weight (SDW), total dry weight (TDW), and root dry weight (RDW). Composite interval mapping analysis using genotypic data from 194 SNP markers identified six genomic regions associated with traits on chromosomes 3, 4, 5, and 6 with phenotypic variance ranging from 2.5 to 18.6%. Among them 2 QTL regions; one on chr3 (id3001701-id300833) and the other on chr5 (wd5002636-id5001470) were identified as QTL hotspots A and B respectively and expressed consistently in field as well as glasshouse condition. The majority of QTLs identified for early vigor, and related traits were clustered in the QTL hotspots A (qEV3.1, qEUE3.1, qSHL3.1, qSL3.1, qSFW3.1, qTFW3.1, qRDW3.1 ) and QTL hotspot B (qEV5.1, qEUE5.1, qSHL5.1, qSL5.1, qSFW5.1, qSDW5.1, qTDW5.1 ). Ten putative candidate genes viz., 1-alpha-amylase precursor, 2-glutamate decarboxylase, 1-ethylene-insensitive 3, 3-expansin precursor, and 3-phenylalanine ammonia-lyase associated with the target traits were identified in the selected QTL regions. Mutations were identified in the coding region of alpha-amylase precursor and ethylene-insensitive 3 gene between the parents which can be utilized in marker assisted breeding. Trait relationships among the agro-physiological traits were examined to select the best genotypes for the given traits for use in future breeding programs.

Genetic Modification for Improving Seed Vigor Is Transitioning from Model Plants to Crop Plants

Although seed vigor is a complex physiological trait controlled by quantitative trait loci, technological advances in the laboratory are being translated into applications for enhancing seed vigor in crop plants. In this article, we summarize and discuss pioneering work in the genetic modification of seed vigor, especially through the over-expression of protein L-isoaspartyl methyltransferase (PIMT, EC 2.1.1.77) in seeds. The impressive success in improving rice seed vigor through the over-expression of PIMT provides a valuable reference for engineering high-vigor seeds for crop production. In recent decades, numerous genes/proteins associated with seed vigor have been identified. It is hoped that such potential candidates may be used in the development of genetically edited crops for a high and stable yield potential in crop production. This possibility is very valuable in the context of a changing climate and increasing world population.

Identification of genes involved in rice seed priming in the early imbibition stage

Phase II of seed imbibition is a critical process during seed priming. To identify genes involved in rice seed priming, the altered proteins between the dry and imbibed (24 h) seeds were compared using a two-dimensional gel electrophoresis system in this study. Ten significantly changed proteins (fold change ≥ twofold; P < 0.01) were successfully identified, which could be categorised as carbohydrate and protein biosynthesis and metabolism-related, signalling-related, storage and stress-related proteins. A meta-analysis indicated that the highest expression of the identified genes was at the milk and dough stages and in the endosperm tissue. Quantitative real-time PCR analysis showed that there was significant variation in gene expression (except FAD-dependent oxidoreductase) in embryos during seed priming (0-48 h). The expression of genes associated with stress appeared at the early imbibition stage, while those associated with carbohydrate metabolism, protein synthesis and signalling increased at the late imbibition stage. Three identified proteins (glucose-1-phosphate adenylyltransferase large subunit, aminotransferase and prolamin precursor) had similar transcript and protein expression patterns in embryos. Based on phenotype and gene expression, the optimal stop time for seed priming is 24 h, when these three genes have relatively low expression, followed by significant induction during imbibition in embryos. These three genes are ideal candidate biomarkers for rice seed priming.

Seedling Emergence and Phenotypic Response of Common Bean Germplasm to Different Temperatures under Controlled Conditions and in Open Field

Rapid and uniform seed germination and seedling emergence under diverse environmental conditions is a desirable characteristic for crops. Common bean genotypes (Phaseolus vulgaris L.) differ in their low temperature tolerance regarding growth and yield. Cultivars tolerant to low temperature during the germination and emergence stages and carriers of the grain quality standards demanded by consumers are needed for the success of the bean crop. The objectives of this study were (i) to screen the seedling emergence and the phenotypic response of bean germplasm under a range of temperatures in controlled chamber and field conditions to display stress-tolerant genotypes with good agronomic performances and yield potential, and (ii) to compare the emergence of bean seedlings under controlled environment and in open field conditions to assess the efficiency of genebanks standard germination tests for predicting the performance of the seeds in the field. Three trials were conducted with 28 dry bean genotypes in open field and in growth chamber under low, moderate, and warm temperature. Morpho-agronomic data were used to evaluate the phenotypic performance of the different genotypes. Cool temperatures resulted in a reduction of the rate of emergence in the bean genotypes, however, emergence and early growth of bean could be under different genetic control and these processes need further research to be suitably modeled. Nine groups arose from the Principal Component Analysis (PCA) representing variation in emergence time and proportion of emergence in the controlled chamber and in the open field indicating a trend to lower emergence in large and extra-large seeded genotypes. Screening of seedling emergence and phenotypic response of the bean germplasm under a range of temperatures in controlled growth chambers and under field conditions showed several genotypes, as landraces 272, 501, 593, and the cultivar Borlotto, with stress-tolerance at emergence, and high yield potential that could be valuable genetic material for breeding programs. Additionally, the potential genetic erosion in genebanks was assessed. Regarding bean commercial traits, under low temperature at sowing time seed reached larger size, and crop yield was higher compared to warmer temperatures at the sowing time. Therefore, early sowing of bean is strongly recommended.

Population Structure, Diversity and Trait Association Analysis in Rice (Oryza sativa L.) Germplasm for Early Seedling Vigor (ESV) Using Trait Linked SSR Markers

Early seedling vigor (ESV) is the essential trait for direct seeded rice to dominate and smother the weed growth. In this regard, 629 rice genotypes were studied for their morphological and physiological responses in the field under direct seeded aerobic situation on 14th, 28th and 56th days after sowing (DAS). It was determined that the early observations taken on 14th and 28th DAS were reliable estimators to study ESV as compared to 56th DAS. Further, 96 were selected from 629 genotypes by principal component (PCA) and discriminate function analyses. The selected genotypes were subjected to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic by using ESV QTL linked simple sequence repeat (SSR) markers. To assess the genetic structure, model and distance based approaches were used. Genotyping of 96 rice lines using 39 polymorphic SSRs produced a total of 128 alleles with the phenotypic information content (PIC) value of 0.24. The model based population structure approach grouped the accession into two distinct populations, whereas unrooted tree grouped the genotypes into three clusters. Both model based and structure based approach had clearly distinguished the early vigor genotypes from non-early vigor genotypes. Association analysis revealed that 16 and 10 SSRs showed significant association with ESV traits by general linear model (GLM) and mixed linear model (MLM) approaches respectively. Marker alleles on chromosome 2 were associated with shoot dry weight on 28 DAS, vigor index on 14 and 28 DAS. Improvement in the rate of seedling growth will be useful for identifying rice genotypes acquiescent to direct seeded conditions through marker-assisted selection.

Genetic dissection of maize seedling root system architecture traits using an ultra-high density bin-map and a recombinant inbred line population

Maize (Zea mays) root system architecture (RSA) mediates the key functions of plant anchorage and acquisition of nutrients and water. In this study, a set of 204 recombinant inbred lines (RILs) was derived from the widely adapted Chinese hybrid ZD958(Zheng58 × Chang7-2), genotyped by sequencing (GBS) and evaluated as seedlings for 24 RSA related traits divided into primary, seminal and total root classes. Significant differences between the means of the parental phenotypes were detected for 18 traits, and extensive transgressive segregation in the RIL population was observed for all traits. Moderate to strong relationships among the traits were discovered. A total of 62 quantitative trait loci (QTL) were identified that individually explained from 1.6% to 11.6% (total root dry weight/total seedling shoot dry weight) of the phenotypic variation. Eighteen, 24 and 20 QTL were identified for primary, seminal and total root classes of traits, respectively. We found hotspots of 5, 3, 4 and 12 QTL in maize chromosome bins 2.06, 3.02-03, 9.02-04, and 9.05-06, respectively, implicating the presence of root gene clusters or pleiotropic effects. These results characterized the phenotypic variation and genetic architecture of seedling RSA in a population derived from a successful maize hybrid.

Genetic Components of Heterosis for Seedling Traits in an Elite Rice Hybrid Analyzed Using an Immortalized F2 Population

Utilization of heterosis has greatly contributed to rice productivity in China and many Asian countries. Superior hybrids usually show heterosis at two stages: canopy development at vegetative stage and panicle development at reproductive stage resulting in heterosis in yield. Although the genetic basis of heterosis in rice has been extensively investigated, all the previous studies focused on yield traits at maturity stage. In this study, we analyzed the genetic basis of heterosis at seedling stage making use of an "immortalized F2" population composed of 105 hybrids produced by intercrossing recombinant inbred lines (RILs) from a cross between Zhenshan 97 and Minghui 63, the parents of Shanyou 63, which is an elite hybrid widely grown in China. Eight seedling traits, seedling height, tiller number, leaf number, root number, maximum root length, root dry weight, shoot dry weight and total dry weight, were investigated using hydroponic culture. We analyzed single-locus and digenic genetic effects at the whole genome level using an ultrahigh-density SNP bin map obtained by population re-sequencing. The analysis revealed large numbers of heterotic effects for seedling traits including dominance, overdominance and digenic dominance (epistasis) in both positive and negative directions. Overdominance effects were prevalent for all the traits, and digenic dominance effects also accounted for a large portion of the genetic effects. The results suggested that cumulative small advantages of the single-locus effects and two-locus interactions, most of which could not be detected statistically, could explain the genetic basis of seedling heterosis of the F1 hybrid.