Resequencing Reveals Different Domestication Rate for BADH1 and BADH2 in Rice (Oryza sativa)

De novo creation of popcorn-like fragrant foxtail millet

Popcorn aroma is a valuable flavor quality in cereals, but, despite more than ten thousand years of millet domestication, millet lacks traits that confer this desirable aroma. Here, we developed a popcorn-scented millet, providing an important resource for future breeding.

Gene Genealogy-Based Mutation Analysis Reveals Emergence of Aus, Tropical japonica, and Aromatic of Oryza sativa during the Later Stage of Rice Domestication

Asian rice (Oryza sativa L.) has become a model for understanding gene functions and domestication in recent decades; however, its own diversification is still controversial. Although the division of indica and japonica and five subgroups (aus, indica (sensu stricto), japonica (sensu stricto), tropical japonica, and aromatic) are broadly accepted, how they are phylogenetically related is not transparent. To clarify their relationships, a sample of 121 diverse genes was chosen here from 12 Oryza genomes (two parental and ten O. sativa (Os)) in parallel to allow gene genealogy-based mutation (GGM) analysis. From the sample, 361 Os mutations were shared by two or more subgroups (referred to here as trans mutations) from 549 mutations identified at 51 Os loci. The GGM analysis and related tests indicates that aus diverged from indica at a time significantly earlier than when tropical japonica split from japonica. The results also indicate that aromatic was selected from hybrid progeny of aus and tropical japonica and that all five subgroups share a significant number of the early mutations identified previously. The results suggest that aus, tropical japonica, and aromatic emerged sequentially within the most recent 4-5 millennia of rice domestication after the split of indica and japonica.

Combined Metabolomic and Quantitative RT-PCR Analyses Revealed the Synthetic Differences of 2-Acetyl-1-pyrroline in Aromatic and Non-Aromatic Vegetable Soybeans

Aroma is an important economic trait of vegetable soybeans, which greatly influences their market value. The 2-acetyl-1-pyrroline (2AP) is considered as an important substance affecting the aroma of plants. Although the 2AP synthesis pathway has been resolved, the differences of the 2AP synthesis in the aromatic and non-aromatic vegetable soybeans are unknown. In this study, a broad targeted metabolome analysis including measurement of metabolites levels and gene expression levels was performed to reveal pathways of aroma formation in the two developmental stages of vegetable soybean grains [35 (S5) and 40 (S6) days after anthesis] of the 'Zhexian No. 8' (ZX8, non-aromatic) and ZK1754 (aromatic). The results showed that the differentially accumulated metabolites (DAMs) of the two varieties can be classified into nine main categories including flavonoids, lipids, amino acids and derivatives, saccharides and alcohols, organic acids, nucleotides and derivatives, phenolic acids, alkaloids and vitamin, which mainly contributed to their phenotypic differences. Furthermore, in combination with the 2AP synthesis pathway, the differences of amino acids and derivatives were mainly involved in the 2AP synthesis. Furthermore, 2AP precursors' analysis revealed that the accumulation of 2AP mainly occurred from 1-pyrroline-5-carboxylate (P5C), not 4-aminobutyraldehyde (GABald). The quantitative RT-PCR showed that the associated synthetic genes were 1-pyrroline-5-carboxylate dehydrogenase (P5CDH), ∆¹-pyrroline-5-carboxylate synthetase (P5CS), proline dehydrogenase (PRODH) and pyrroline-5-carboxylate reductase (P5CR), which further verified the synthetic pathway of 2AP. Furthermore, the betaine aldehyde dehydrogenase 2 (GmBADH2) mutant was not only vital for the occurrence of 2AP, but also for the synthesis of 4-aminobutyric acid (GABA) in vegetable soybean. Therefore, the differences of 2AP accumulation in aromatic and non-aromatic vegetable soybeans have been revealed, and it also provides an important theoretical basis for aromatic vegetable soybean breeding.

Insights of Improved Aroma under Additional Nitrogen Application at Booting Stage in Fragrant Rice

Plant mineral nutrition substantially affects the growth, yield and quality of rice, whereas nitrogen (N) application contributes significantly in this regard. Undoubtedly, N application improves rice aroma biosynthesis; however, the molecular mechanism underlying the regulation of grain 2-acetyl-1-pyrroline (2-AP) biosynthesis in the presence of nitrogen application at the booting stage has remained largely unexplored. The present study examined the effects of three N levels, i.e., 0 g per pot (N0), 0.43 g per pot (N1) and 0.86 g per pot (N2) on intermediates, enzymes and genes involved in 2-AP biosynthesis, as well as on the yield of two fragrant rice cultivars viz, Meixiangzhan2 and Xiangyaxiangzhan. N was additionally applied at the booting stage. The results depicted that the levels of precursor, such as proline, and the activity of enzymes involved in 2-AP biosynthesis, such as Δ1-pyrroline-5-carboxylate synthetase (P5CS) and diamine oxidase (DAO), and P5CS1 gene expression were comparatively higher under N1 than N0 in both fragrant rice cultivars. Moreover, the N2 treatment increased the grain panicle-1, filled grain percentage and grain yield of both rice cultivars, while the grain yield of Meixiangzhan2 and Xiangyaxiangzhan was increased by 15.87% and 12.09%, respectively, under N2 compared to N1 treatment. Hence, 0.43 g per pot of N showed positive performances in yield and aroma accumulation in fragrant rice and should be further employed in the practice and production for better cultivation in the rice market.

Molecular profiling of BADH2 locus reveals distinct functional allelic polymorphism associated with fragrance variation in Indian aromatic rice germplasm

Allelic variability of the aroma gene, betaine aldehyde dehydrogenase 2 (BADH2) was studied in a random subset of indigenous aromatic rice germplasm along with a few exotic aromatic accessions. Use of functional markers of four badh2 alleles identified that the test panel possessed only two alleles, badh2-E7 and badh2-p-5'UTR. Two other alleles, badh2.2 and badh2-E4-5.2 were absent. Based on the alleles present, four functional polymorphisms (FP) were detected, namely FP1 to FP4. 188 genotypes possessed FP1 having both the badh2-p-5'UTR and badh2-E7 (71.8%) alleles. The badh2 allele with FP1 is named badh2-E7-p. 39 genotypes (14.9%) possessed only the badh2-p-5'UTR allele (FP3), while three genotypes were found to carry only the badh2-E7 allele (FP2). We also found that 32 genotypes (12.2%) did not have any of the target aroma alleles tested in this study (FP4). Interestingly, for badh2-p-5'UTR marker, the expected 198 bp amplicon for the non-aromatic allele could not be detected among any of the genotypes tested. Instead, an amplicon of 456 bp length appeared with 100% presence in the non-aromatic checks. Notwithstanding, the 456 bp allele also showed a 16% presence among the aromatic lines. This article forms the first report of this allele, named badh2-p1, among aromatic rice. Quantification of 2-Acetyl-1-Pyrroline (2AP) content and sensory evaluation among the test genotypes showed that those with FP1 are highly aromatic than the genotypes carrying other types of FPs. But, a few strongly aromatic lines showed lower 2AP content. The BADH2 characterization carried out in this study is suggestive of identifying the additional gene(s)/ allele(s) governing aroma among the Indian fragrant rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01181-9.

Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication

Betaine aldehyde dehydrogenase 1 (BADH1), a paralog of the fragrance gene BADH2, is known to be associated with salt stress through the accumulation of synthesized glycine betaine (GB), which is involved in the response to abiotic stresses. Despite the unclear association between BADH1 and salt stress, we observed the responses of eight phenotypic characteristics (germination percentage (GP), germination energy (GE), germination index (GI), mean germination time (MGT), germination rate (GR), shoot length (SL), root length (RL), and total dry weight (TDW)) to salt stress during the germination stage of 475 rice accessions to investigate their association with BADH1 haplotypes. We found a total of 116 SNPs and 77 InDels in the whole BADH1 gene region, representing 39 haplotypes. Twenty-nine haplotypes representing 27 mutated alleles (two InDels and 25 SNPs) were highly (p < 0.05) associated with salt stress, including the five SNPs that have been previously reported to be associated with salt tolerance. We observed three predominant haplotypes associated with salt tolerance, Hap_2, Hap_18, and Hap_23, which were Indica specific, indicating a comparatively high number of rice accessions among the associated haplotypes. Eight plant parameters (phenotypes) also showed clear responses to salt stress, and except for MGT (mean germination time), all were positively correlated with each other. Different signatures of domestication for BADH1 were detected in cultivated rice by identifying the highest and lowest Tajima’s D values of two major cultivated ecotypes (Temperate Japonica and Indica). Our findings on these significant associations and BADH1 evolution to plant traits can be useful for future research development related to its gene expression.

Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA

Knowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, 214 potato clones were genotyped with the Infinium Illumina 22 K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components. The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.

Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (Gossypium hirsutum L.)

Although upland cotton (Gossypium hirsutism L.) originated in the tropics, this early maturity cotton can be planted as far north as 46°N in China due to the accumulation of numerous phenotypic and physiological adaptations during domestication. However, how the genome of early maturity cotton has been altered by strong human selection remains largely unknown. Herein, we report a cotton genome variation map generated by the resequencing of 436 cotton accessions. Whole-genome scans for sweep regions identified 357 putative selection sweeps covering 4.94% (112 Mb) of the upland cotton genome, including 5184 genes. These genes were functionally related to flowering time control, hormone catabolism, ageing and defence response adaptations to environmental changes. A genome-wide association study (GWAS) for seven early maturity traits identified 307 significant loci, 22.48% (69) of which overlapped with putative selection sweeps that occurred during the artificial selection of early maturity cotton. Several previously undescribed candidate genes associated with early maturity were identified by GWAS. This study provides insights into the genetic basis of early maturity in upland cotton as well as breeding resources for cotton improvement.

Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding

Recent next generation sequencing-driven mass production of genomic data and multi-omics-integrated approaches have significantly contributed to broadening and deepening our knowledge on the molecular system of living organisms. Accordingly, translational genomics (TG) approach can play a pivotal role in creating an informational bridge between model systems and relatively less studied plants. This review focuses mainly on addressing recent advancement in omics-related technologies, a diverse array of bioinformatic resources and potential applications of TG for the crop breeding. To accomplish above objectives, information on omics data production, various DBs and high throughput technologies was collected, integrated, and used to analyze current status and future perspectives towards omics-assisted crop breeding. Various omics data and resources have been organized and integrated into the databases and/or bioinformatic infrastructures, and thereby serve as the ome's information center for cross-genome translation of biological data. Although the size of accumulated omics data and availability of reference genomes are different among plant families, translational approaches have been actively progressing to access particular biological characteristics. When multi-layered omics data are integrated in a synthetic manner, it will allow providing a stereoscopic view of dynamic molecular behavior and interacting networks of genes occurring in plants. Consequently, TG approach will lead us to broader and deeper insights into target traits for the plant breeding. Furthermore, such systems approach will renovate conventional breeding programs and accelerate precision crop breeding in the future.

Molecular basis for increased 2-acetyl-1-pyrroline contents under alternate wetting and drying (AWD) conditions in fragrant rice

Factors affecting rice aroma biosynthesis have been well documented previously, however the molecular mechanism lies behind the regulations in grain 2-acetyl-1-pyrroline (2AP) biosynthesis under alternate wetting and drying (AWD) remained largely unexplored. Present study investigated the effects of three irrigation regimes i.e., conventional irrigation (CI), alternate wetting and moderate drying (WMD), and alternate wetting and severe drying (WSD) on the yield, quality traits, intermediates, enzyme activities and genes involved in 2-acetyl-1-pyrroline biosynthesis in two fragrant rice cultivars viz, Meixiangzhan2 and Xiangyaxiangzhan. Results revealed that the levels of intermediates such as Δ1-pyrroline-5-carboxylate (P5C) and Δ1-pyrroline, and the activity of enzymes such as proline dehydrogenase (PRODH), Δ1-pyrroline-5-carboxylate synthetase (P5CS), diamine oxidase (DAO), and gene expressions of PRODH, P5CS2 and DAO were comparatively higher under AWD than CI in both aromatic rice cultivars. The levels of gamma-aminobutyric acid (GABA), betaine aldehyde dehydrogenase 2 (BADH2) and BADH2 gene were lower that together led to enhanced 2-AP contents in rice grains. Moreover, WMD irrigation improved yield and yield characters, while WSD irrigation reduced yield and quality traits of rice. Overall, up-regulation of P5C and Δ1-pyrroline and down-regulation of GABA under AWD treatments resulted in enhanced 2AP biosynthesis in both rice cultivars. Evaluation and adoption of AWD (within safe limits) at field level could be an alternative option to conventional flooded rice to get better yield and quality.

Effects of milling on aromatics, lipophilic phytonutrients, and fatty acids in unprocessed white rice of scented rice 'Cheonjihyang-1-se

To understand effects of milling, scented rice 'Cheonjihyang-1-se' was milled from 10 to 140 s and changes in volatiles, phytonutrients, and fatty acids were evaluated. Among 43 identified odor-active compounds, four volatiles, including hexan-3-one, exhibited decreases of up to 78%, while four others including (E)-non-2-enal, increased following milling. Levels of 2-acetyl-1-pyrroline, the most distinctive popcorn-flavoring compound in scented rice, were not affected by the degree of milling (DM). Partial least squares discriminant analyses of volatiles were able to differentiate white rice according to the DM. Benzene and 2-pentylfuran showed the highest variable importance in projection scores, which could be applied in estimating the DM of rice. Milling significantly decreased tocopherols, tocotrienols, squalene, phytosterols contents and oleic acid composition, while palmitic acid composition was increased. These results suggest milling-dependent variations in phytonutrient levels and lipid composition, as well as changes in aroma and subsequent market quality, in 'Cheonjihyang-1-se' rice.

Population genomics identifies the origin and signatures of selection of Korean weedy rice

Weedy rice is the same biological species as cultivated rice (Oryza sativa); it is also a noxious weed infesting rice fields worldwide. Its formation and population-selective or -adaptive signatures are poorly understood. In this study, we investigated the phylogenetics, population structure and signatures of selection of Korean weedy rice by determining the whole genomes of 30 weedy rice, 30 landrace rice and ten wild rice samples. The phylogenetic tree and results of ancestry inference study clearly showed that the genetic distance of Korean weedy rice was far from the wild rice and near with cultivated rice. Furthermore, 537 genes showed evidence of recent positive or divergent selection, consistent with some adaptive traits. This study indicates that Korean weedy rice originated from hybridization of modern indica/indica or japonica/japonica rather than wild rice. Moreover, weedy rice is not only a notorious weed in rice fields, but also contains many untapped valuable traits or haplotypes that may be a useful genetic resource for improving cultivated rice.

Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.)

Background

Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs). In the present study, genome-wide association study with high-quality re-sequencing data was performed for 10 ECQs in a panel of 227 non-glutinous rice accessions and four derived panels.

Results

Population structure accounted for high phenotypic variation in three routine panels and had minor effects on subspecies-based panels. Using the mixed linear model method based on the P + K model, we detected 29, 24, 16, 17, and 29 loci that were significant for ECQ parameters in each of the five panels. Some of these loci were close to starch synthesis-related genes. Two quantitative trait loci (QTLs) (chr.9: 15417525 ~ 15474876; 17538294 ~ 18443016) for several starch paste viscosity properties detected in four panels were close to the isoamylase 3 gene, one QTL (chr.1: 30627943 ~ 31668474) for consistency detected in three panels was close to the starch synthase IV-1 gene. The QTL (chr.7: 1118122 ~ 1967247) for breakdown (BD), detected in the whole panel and japonica panel, and one QTL (chr.7: 25312126 ~ 26540950) for BD and setback (SB), detected in the whole panel and indica panel, may be specific gene alleles in japonica or indica panels. One previously detected QTL (chr.11: 22240707 ~ 22563596) for protein content and one new QTL (chr.5: 7756614 ~ 8042699) for many ECQ traits detected in more than two panels, may represent valuable targets for future cloning of the underlying genes.

Conclusions

This study detected minor-effect QTLs affecting ECQs, and may increase our understanding of the genetic differences regulating the formation of ECQ between indica and japonica varieties.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3000-z) contains supplementary material, which is available to authorized users.

Genome-wide Association Mapping of Polyphenol Contents and Antioxidant Capacity in Whole-Grain Rice

Whole grains contain various bioactive phytochemicals including phenolic acids, and consumption of whole grains may provide desirable health benefits and reduce the risks of chronic diseases due to their antioxidant activities. In this study, we qualified and quantified 9 bound phenolic compounds in 32 red and 88 white pericarp accessions of rice. A genome-wide association study (GWAS) was conducted for free (FP) and bound (BP) phenolic compounds and their antioxidant capacities with high-quality single-nucleotide polymorphisms (SNPs) in two colored grain panels and the whole panel. Rc was detected for all FP and antioxidant capacities in the whole panel. Three loci (chr.1:30970095, chr.6:24392269, and chr.9:6670223) for more than five phenolic-related traits, two loci (chr.4:34120529 and chr.11:28947480) for more than two FP-related traits, and one locus (chr.11:23220681) for ferulic acid detected in two panels were potentially new genes that are valuable for further gene cloning. Overall, this study increases our understanding on the genetics of phenolic acid biosynthesis in the phenylpropanoid pathway.