Maturity Loci Research Articles

Expression, purification and crystallization of the photosensory module of phytochrome B (phyB) from Sorghum bicolor.

Sorghum, a short-day tropical plant, has been adapted for temperate grain production, in particular through the selection of variants at the MATURITY loci (Ma1-Ma6) that reduce photoperiod sensitivity. Ma3 encodes phytochrome B (phyB), a red/far-red photochromic biliprotein photoreceptor. The multi-domain gene product, comprising 1178 amino acids, autocatalytically binds the phytochromobilin chromophore to form the photoactive holophytochrome (Sb.phyB). This study describes the development of an efficient heterologous overproduction system which allows the production of large quantities of various holoprotein constructs, along with purification and crystallization procedures. Crystals of the Pr (red-light-absorbing) forms of NPGP, PGP and PG (residues 1-655, 114-655 and 114-458, respectively), each C-terminally tagged with His6, were successfully produced. While NPGP crystals did not diffract, those of PGP and PG diffracted to 6 and 2.1 Å resolution, respectively. Moving the tag to the N-terminus and replacing phytochromobilin with phycocyanobilin as the ligand produced PG crystals that diffracted to 1.8 Å resolution. These results demonstrate that the diffraction quality of challenging protein crystals can be improved by removing flexible regions, shifting fusion tags and altering small-molecule ligands.

The genetic architecture of soybean photothermal adaptation to high latitudes.

Soybean is a major plant protein source for both human food and animal feed, but to meet global demands as well as a trend towards regional production, soybean cultivation needs to be expanded to higher latitudes. In this study, we developed a large diversity panel consisting of 1503 early-maturing soybean lines and used genome-wide association mapping to dissect the genetic architecture underlying two crucial adaptation traits, flowering time and maturity. This revealed several known maturity loci, E1, E2, E3, and E4, and the growth habit locus Dt2 as causal candidate loci, and also a novel putative causal locus, GmFRL1, encoding a homolog of the vernalization pathway gene FRIGIDA-like 1. In addition, the scan for quantitative trait locus (QTL)-by-environment interactions identified GmAPETALA1d as a candidate gene for a QTL with environment-dependent reversed allelic effects. The polymorphisms of these candidate genes were identified using whole-genome resequencing data of 338 soybeans, which also revealed a novel E4 variant, e4-par, carried by 11 lines, with nine of them originating from Central Europe. Collectively, our results illustrate how combinations of QTL and their interactions with the environment facilitate the photothermal adaptation of soybean to regions far beyond its center of origin.

Progress and Prospects of the Molecular Basis of Soybean Cold Tolerance.

Cold stress is a major factor influencing the geographical distribution of soybean growth and causes immense losses in productivity. Understanding the molecular mechanisms that the soybean has undergone to survive cold temperatures will have immense value in improving soybean cold tolerance. This review focuses on the molecular mechanisms involved in soybean response to cold. We summarized the recent studies on soybean cold-tolerant quantitative trait loci (QTLs), transcription factors, associated cold-regulated (COR) genes, and the regulatory pathways in response to cold stress. Cold-tolerant QTLs were found to be overlapped with the genomic region of maturity loci of E1, E3, E4, pubescence color locus of T, stem growth habit gene locus of Dt1, and leaf shape locus of Ln, indicating that pleiotropic loci may control multiple traits, including cold tolerance. The C-repeat responsive element binding factors (CBFs) are evolutionarily conserved across species. The expression of most GmDREB1s was upregulated by cold stress and overexpression of GmDREB1B;1 in soybean protoplast, and transgenic Arabidopsis plants can increase the expression of genes with the DRE core motif in their promoter regions under cold stress. Other soybean cold-responsive regulators, such as GmMYBJ1, GmNEK1, GmZF1, GmbZIP, GmTCF1a, SCOF-1 and so on, enhance cold tolerance by regulating the expression of COR genes in transgenic Arabidopsis. CBF-dependent and CBF-independent pathways are cross-talking and work together to activate cold stress gene expression. Even though it requires further dissection for precise understanding, the function of soybean cold-responsive transcription factors and associated COR genes studied in Arabidopsis shed light on the molecular mechanism of cold responses in soybeans and other crops. Furthermore, the findings may also provide practical applications for breeding cold-tolerant soybean varieties in high-latitude and high-altitude regions.

Molecular characterization of E1 and E3 maturity loci of soybean [Glycine Max (L.) merrill] genotypes with contrasting maturity

Molecular characterization of E1 and E3 maturity loci of soybean [Glycine Max (L.) merrill] genotypes with contrasting maturity

Genetic mapping of host resistance to soybean sudden death syndrome

AbstractSoybean sudden death syndrome (SDS) is a disease caused by a soil‐borne fungus, Fusarium virguliforme. Many genetic studies have attempted to identify genes responsible for the quantitative host resistance to SDS. Three recombinant inbred line (RIL) populations were evaluated for foliar SDS resistance at a naturally infested field site in Decatur, MI, during the 2014 and 2015 growing seasons. Lines were evaluated for disease severity (DS) on a 1–9 scale, disease incidence (DI) as an estimate of the percentage of plants with symptoms per plot, and disease index (DX) as a metric which integrates DS and DI. Phenotypic data was spatially adjusted to account for uneven pathogen distribution in the naturally infested field. A subset of RILs from each population were genotyped with the SoySNP6K Illumina Infinium BeadChip. Linkage maps unique to each population were constructed using JoinMap ver. 2. Composite interval mapping was performed using WinQTLCartographer ver. 2.5. Three quantitative trait loci (QTL) were identified across 2 yr and/or multiple populations. One QTL on Chromosome 10 appeared to be colocalized with the E2 maturity locus. Another QTL identified was on Chromosome 18, in a region which has been demonstrated to provide soybean cyst nematode (SCN) and SDS resistance in many studies (rhg1/Rfs2).

Genetic control and allele variation among soybean maturity groups 000 through IX

Soybean [Glycinemax (L.) Merr.] maturity determines the growing region of a given soybean variety and is a primary factor in yield and other agronomic traits. The objectives of this research were to identify the quantitative trait loci (QTL) associated with maturity groups (MGs) and determine the genetic control of soybean maturity in each MG. Using data from 16,879 soybean accessions, genome-wide association (GWA) analyses were conducted for each paired MG and across MGs 000 through IX. Genome-wide association analyses were also performed using 184 genotypes (MGs V-IX) with days to flowering (DTF) and maturity (DTM) collected in the field. A total of 58 QTL were identified to be significantly associated with MGs in individual GWAs, which included 12 reported maturity loci and two stem termination genes. Genome-wide associations across MGs 000-IX detected a total of 103 QTL and confirmed 54 QTL identified in the individual GWAs. Of significant loci identified, qMG-5.2 had effects on the highest number (9) of MGs, followed by E2, E3, Dt2, qMG-15.5, E1, qMG-13.1, qMG-7.1, and qMG-16.1, which affected five to seven MGs. A high number of genetic loci (8-25) that affected MGs 0-V were observed. Stem termination genes Dt1 and Dt2 mainly had significant allele variation in MGs II-V. Genome-wide associations for DTF, DTM, and reproductive period (RP) in the diversity panel confirmed 15 QTL, of which seven were observed in MGs V-IX. The results generated can help soybean breeders manipulate the maturity loci for genetic improvement of soybean yield.

Allelic Variation of Soybean Maturity Genes E1–E4 in the Huang-Huai-Hai River Valley and the Northwest China

Soybean is planted in a wide span of the world, and flowering and maturity time is an important trait determining soybean yield formation and adaptation. Maturity loci E1, E2, E3 and E4 were frequently reported as the most influential genetic loci for soybean flowering and maturity. To understand the allelic variation and assess the phenological traits of cultivars with different E allelic combinations in natural environments, 251 cultivars of maturity group (MG) I–V were field tested in 42 locations across four sub-regions in the Huang-Huai-Hai and Northwest region of China and genotyped with KASP markers for E1–E4 loci. The results indicated that mutant alleles were only found in the E1 and E2 locus, all of the cultivars carried functional alleles in the E3 and E4 loci in this area, with the frequency of mutant allele to be higher in early maturity groups (MGs) than late MGs. Among nine E allelic combinations in this area, one photoperiodic insensitive mutation in E2 loci (E1/e2-ns/E3-Ha/E4 and E1/e2-ns/E3-Mi/E4) made up the largest proportion (25.10 and 18.33%), while two photoperiodic insensitive mutations in both E1 and E2 loci (e1-as/e2-ns/E3-Ha/E4) (1.20%) occupied the lowest proportion in this panel. The major combinations of E locus for MGI, MGII and MG III in this area were E1/E2-dl/E3-Mi/E4, E1/e2-ns/E3-Mi/E4 and E1/e2-ns/E3-Ha/E4, respectively. Cultivars carrying e1-as/e2-ns/E3-Ha/E4 genotype flowered earliest (34 days) on average, 7.6 days earlier than the latest-flowering E haplotype (E1/e2-ns/E3-Ha/E4). This study provided an opportunity to detect the E allelic combinations in the Huang-Huai-Hai River Valley and the Northwest China, which would facilitate the improvement of soybean adaptation in the future.

The Synchronized Efforts to Decipher the Molecular Basis for Soybean Maturity Loci E1, E2, and E3 That Regulate Flowering and Maturity.

The general concept of photoperiodism, i.e., the photoperiodic induction of flowering, was established by Garner and Allard (1920). The genetic factor controlling flowering time, maturity, or photoperiodic responses was observed in soybean soon after the discovery of the photoperiodism. E1, E2, and E3 were named in 1971 and, thereafter, genetically characterized. At the centennial celebration of the discovery of photoperiodism in soybean, we recount our endeavors to successfully decipher the molecular bases for the major maturity loci E1, E2, and E3 in soybean. Through systematic efforts, we successfully cloned the E3 gene in 2009, the E2 gene in 2011, and the E1 gene in 2012. Recently, successful identification of several circadian-related genes such as PRR3a, LUX, and J has enriched the known major E1-FTs pathway. Further research progresses on the identification of new flowering and maturity-related genes as well as coordinated regulation between flowering genes will enable us to understand profoundly flowering gene network and determinants of latitudinal adaptation in soybean.

Identifying new variation at the J locus, previously identified as e6, in long juvenile \u2018Paranagoiana\u2019 soybean

Key messageA previously identified soybean maturity locus, E6, is discovered to be J, with the long juvenile allele in Paranagoiana now deemed j−x.Soybean grown at latitudes of ~20° or lower can produce lower grain yields due to the short days. This limitation can be overcome by using the long juvenile trait (LJ) which delays flowering under short day conditions. Two LJ loci have been mapped to the same location on Gm04, J and E6. The objective of this research was to investigate the e6 allele in ‘Paranagoiana’ and determine if E6 and J are the same locus or linked loci. KASP markers showed that e6 lines did not have the j−1 allele of LJ PI 159925. A population fixed for E1 but segregating for E6, with e6 introgressed from Paranagoiana, showed single gene control for flowering and maturity under short days. Sequencing Glyma.04G050200, the J gene, with long amplification Taq found that the e6 line ‘Paranagoiana’ contains a Ty1-copia retrotransposon of ~10,000 bp, inserted within exon 4. PCR amplification of the cDNA of Glyma.04G050200 also showed differences between the mRNA sequences (presence of insertion in j−x). Hence, we conclude that the loci E6 and J are one locus and deem this new variation found in Paranagoiana as j−x.

High-density linkage map reveals QTL for Type-I seed coat cracking in RIL population of soybean [Glycine max (L.) Merr.

Seed coat cracking (SCC), particularly the Type-I irregular cracking, is critical in determining the quality of appearance and commercial value of soybean seeds. The objective of this study was to identify the quantitative trait loci (QTLs) for SCC with high-density genetic map. One hundred sixty-seven recombinant inbred lines (RILs) developed from a cross between Uram (SCC-resistant) and Chamol (SCC-susceptible) were evaluated for SCC over 2 years (2016–2017). The QTL analysis identified 12 QTLs located on chromosomes 2 (D1b), 6 (C2), 8 (A2), 9 (K), 10 (O), 12 (H), 19 (L), and 20 (I). Out of the 12 QTLs, qSC2-1, qSC9, SC10-1, qSC10-2, and qSC12 were novel QTLs and the other seven QTLs (qSC2-2, qSC2-3, qSC6, qSC8, qSC19-1, qSC19-2, and qSC20) were found to co-localize with the previously identified QTLs. The mean SCC of the RILs of early maturity group was significantly higher than that of the late maturity group, suggesting an association between SCC and maturity loci. In addition, although 10 QTLs were distantly located from the maturity loci (E1, E3, E4, E7, and E10), qSC10-1 and qSC10-2 co-localized with the maturity loci E2. The results obtained in this study provide useful genetic information on SCC which could be used in the SCC breeding programs.

Identification of Non-Pleiotropic Loci in Flowering and Maturity Control in Soybean

Pleiotropy is considered to have a significant impact on multi-trait evolution, but its roles in the evolution of domestication-related traits in crop species have been unclear. In soybean, several known quantitative trait loci (QTL) controlling maturity, called the maturity loci, are known to have major effects on both flowering and maturity in a highly correlated pleiotropic manner. Aiming at the identification of non-pleiotropic QTLs that independently control flowering and maturity and dissecting the effects of pleiotropy in these important agronomic traits, we conducted a QTL mapping experiment by creating a population from a cross between domesticated soybean G. max and its wild ancestor G. soja that underwent stringent selection for non-pleiotropy in flowering and maturity. Our QTL mapping analyses using the experimental population revealed novel loci that acted in a non-pleiotropic manner: R1-1 controlled primarily flowering and R8-1 and R8-2 controlled maturity, while R1-1 overlapped with QTL, affecting other agronomic traits. Our results suggest that pleiotropy in flowering and maturity can be genetically separated, while artificial selection during soybean domestication and diversification may have favored pleiotropic loci such as E loci that control both flowering and maturity. The non-pleiotropic loci identified in this study will help to identify valuable novel genes to optimize soybean’s life history traits and to improve soybean’s yield potential under diverse environments and cultivation schemes.

Abstract 4492: Characterization of the T-Cell receptor repertoire in patients with acute myeloid leukemia treated with 5-Azacytidine plus chemotherapy

Abstract Acute Myeloid Leukemia (AML) is a hematological malignancy with a 5 year overall survival of less than 30%. DNA hypomethylating agents such as 5-Azacytidine (5-Aza) have been increasingly used in AML therapy. The effect of hypomethylating agents on T-cell driven anti-leukemia responses remains unclear. For anti-leukemia responses, T-cells must express a T-cell receptor (TCR) with specificity for cancer antigens. TCR recombination, the rearrangement of V, D (beta only) and J segments across the TCR alpha and beta loci into a mature TCR locus, shapes the antigen specificity of TCRs. DNA methylation across the TCR loci may limit the rearrangement of particular V, D, J segments and impact TCR repertoire composition. Whether 5-Aza can alter TCR loci methylation patterns, increase TCR diversity and enhance T-cell driven anti-leukemia responses is unknown. In a cohort of 23 patient with AML, we performed TCR-seq on pre- (diagnostic) and post-therapy (day 5 post 5-Aza) peripheral blood RNA samples obtained from 13 responders and 10 non-responders. Illumina compatible libraries were generated from patient samples using a 5'RACE like approach and sequenced on the MiSeq platform, generating 300x2bp reads. Reads were processed and analyzed using MiXCR and VDJTools, respectively. GraphPad Prism 8 (Two-sided T test) was used for statistical comparisons, P values < 0.05 were considered significant after adjusting for multiple comparisons using the Bonferroni-Dunn method. We obtained an average of 1,146,043 (SD± 767,216) reads and identified an average of 15,732 (SD ± 17,388) clones per sample. We compared pre- and post-therapy TCR diversity among both outcome groups using the Shannon diversity index. TCR diversity did not significantly change following 5-Aza treatment (4827 vs 6159, P= 0.55). Also, TCR diversity was not significantly different between outcome groups pre- and post-therapy. We designated clones as minor (< 10 reads) or major (> 10 reads). We compared pre- and post-therapy minor clone TRBV exon patterns and discovered a 2.2 fold increase in unique clones containing TRBV16 among responders post therapy (P = 0.017). We also observed a 2.5 fold increase in unique clones containing TRBV7-4 in non-responders post therapy (P = 0.034). There were no significant exon pattern changes in non-stratified analysis. When pre-therapy minor clone exon patterns were compared between outcome groups, a higher frequency of unique clones containing TRBV12-2 in responders versus non-responders was observed (2.8 fold, P < 0.001). In addition, we observed a higher frequency of major clones containing TRBV12-5 among responders post therapy (2.4 fold, P = 0.0558). In the pre-therapy samples, there was a higher frequency of clones containing TRBV5-4 among responders compared to non-responders (2.7 fold, P =0.045). In conclusion, changes in TCR repertoire features such as the utilization of specific V exons may associate with response to 5-Azacytidine therapy. Citation Format: John Beckford, Noreen Fulton, Toyosi Odenike, Wendy Stock, Houda Alachkar. Characterization of the T-Cell receptor repertoire in patients with acute myeloid leukemia treated with 5-Azacytidine plus chemotherapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4492.

Transcriptome-Enabled Network Inference Revealed the GmCOL1 Feed-Forward Loop and Its Roles in Photoperiodic Flowering of Soybean.

Photoperiodic flowering, a plant response to seasonal photoperiod changes in the control of reproductive transition, is an important agronomic trait that has been a central target of crop domestication and modern breeding programs. However, our understanding about the molecular mechanisms of photoperiodic flowering regulation in crop species is lagging behind. To better understand the regulatory gene networks controlling photoperiodic flowering of soybeans, we elucidated global gene expression patterns under different photoperiod regimes using the near isogenic lines (NILs) of maturity loci (E loci). Transcriptome signatures identified the unique roles of the E loci in photoperiodic flowering and a set of genes controlled by these loci. To elucidate the regulatory gene networks underlying photoperiodic flowering regulation, we developed the network inference algorithmic package CausNet that integrates sparse linear regression and Granger causality heuristics, with Gaussian approximation of bootstrapping to provide reliability scores for predicted regulatory interactions. Using the transcriptome data, CausNet inferred regulatory interactions among soybean flowering genes. Published reports in the literature provided empirical verification for several of CausNet's inferred regulatory interactions. We further confirmed the inferred regulatory roles of the flowering suppressors GmCOL1a and GmCOL1b using GmCOL1 RNAi transgenic soybean plants. Combinations of the alleles of GmCOL1 and the major maturity locus E1 demonstrated positive interaction between these genes, leading to enhanced suppression of flowering transition. Our work provides novel insights and testable hypotheses in the complex molecular mechanisms of photoperiodic flowering control in soybean and lays a framework for de novo prediction of biological networks controlling important agronomic traits in crops.

Highly multiplexed AmpliSeq technology identifies novel variation of flowering time-related genes in soybean (Glycine max).

Whole-genome re-sequencing is a powerful approach to detect gene variants, but it is expensive to analyse only the target genes. To circumvent this problem, we attempted to detect novel variants of flowering time-related genes and their homologues in soybean mini-core collection by target re-sequencing using AmpliSeq technology. The average depth of 382 amplicons targeting 29 genes was 1,237 with 99.85% of the sequence data mapped to the reference genome. Totally, 461 variants were detected, of which 150 sites were novel and not registered in dbSNP. Known and novel variants were detected in the classical maturity loci—E1, E2, E3, and E4. Additionally, large indel alleles, E1-nl and E3-tr, were successfully identified. Novel loss-of-function and missense variants were found in FT2a, MADS-box, WDR61, phytochromes, and two-component response regulators. The multiple regression analysis showed that four genes—E2, E3, Dt1, and two-component response regulator—can explain 51.1–52.3% of the variation in flowering time of the mini-core collection. Among them, the two-component response regulator with a premature stop codon is a novel gene that has not been reported as a soybean flowering time-related gene. These data suggest that the AmpliSeq technology is a powerful tool to identify novel alleles.

Maturity2, a novel regulator of flowering time in Sorghum bicolor, increases expression of SbPRR37 and SbCO in long days delaying flowering.

Sorghum bicolor is a drought-resilient facultative short-day C4 grass that is grown for grain, forage, and biomass. Adaptation of sorghum for grain production in temperate regions resulted in the selection of mutations in Maturity loci (Ma1 –Ma6) that reduced photoperiod sensitivity and resulted in earlier flowering in long days. Prior studies identified the genes associated with Ma1 (PRR37), Ma3 (PHYB), Ma5 (PHYC) and Ma6 (GHD7) and characterized their role in the flowering time regulatory pathway. The current study focused on understanding the function and identity of Ma2. Ma2 delayed flowering in long days by selectively enhancing the expression of SbPRR37 (Ma1) and SbCO, genes that co-repress the expression of SbCN12, a source of florigen. Genetic analysis identified epistatic interactions between Ma2 and Ma4 and located QTL corresponding to Ma2 on SBI02 and Ma4 on SBI10. Positional cloning and whole genome sequencing identified a candidate gene for Ma2, Sobic.002G302700, which encodes a SET and MYND (SYMD) domain lysine methyltransferase. Eight sorghum genotypes previously identified as recessive for Ma2 contained the mutated version of Sobic.002G302700 present in 80M (ma2) and one additional putative recessive ma2 allele was identified in diverse sorghum accessions.

Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

BackgroundGenome-wide single nucleotide polymorphism (SNP) markers coupled with allele dosage information has emerged as a powerful tool for studying complex traits in cultivated autotetraploid potato (Solanum tuberosum L., 2n = 4× = 48). To date, this approach has been effectively applied to the identification of quantitative trait loci (QTLs) underlying highly heritable traits such as disease resistance, but largely unexplored for traits with complex patterns of inheritance.ResultsIn this study, an F1 tetraploid russet mapping population (162 individuals) was evaluated for multiple quantitative traits over two years and two locations to identify QTLs associated with tuber sugar concentration, processing quality, vine maturity, and other high-value agronomic traits. We report the linkage maps for the 12 potato chromosomes and the QTL location with corresponding genetic models and candidate SNPs explaining the highest phenotypic variation for tuber quality and maturity related traits. Significant QTLs for tuber glucose concentration and tuber fry color were detected on chromosomes 4, 5, 6, 10, and 11. Collectively, these QTLs explained between 24 and 46% of the total phenotypic variation for tuber glucose and fry color, respectively. The QTL on chromosome 10 was associated with apoplastic invertases, with ‘Premier Russet’ contributing the favorable allele for fry processing quality. On chromosome 5, minor-effect QTLs for tuber glucose concentration and fry color co-localized with various major-effect QTLs, including vine maturity, growth habit, tuber shape, early blight (Altenaria tenuis), and Verticillium wilt (Verticillium spp.).ConclusionsLinkage analysis and QTL mapping in a russet mapping population (A05141) using SNP dosage information successfully identified favorable alleles and candidate SNPs for resistance to the accumulation of tuber reducing sugars. These novel markers have a high potential for the improvement of tuber processing quality. Moreover, the discovery of different genetic models for traits with overlapping QTLs at the maturity locus clearly suggests an independent genetic control.

Genetic mapping of quantitative trait loci for tuber-cadmium and zinc concentration in potato reveals associations with maturity and both overlapping and independent components of genetic control.

Cd is a toxic metal, whilst Zn is an essential for plant and human health. Both can accumulate in potato tubers. We examine the genetic control of this process. The aim of this study was to map quantitative trait loci (QTLs) influencing tuber concentrations of cadmium (Cd) and zinc (Zn). We developed a segregating population comprising 188 F1 progeny derived from crossing two tetraploid cultivars exhibiting divergent tuber-Cd-accumulation phenotypes. These progeny were genotyped using the SolCap 8303 SNP array, and evaluated for Cd, Zn, and maturity-related traits. Linkage and QTL mapping were performed using TetraploidSNPMap software, which incorporates all allele dosage information. The final genetic map comprised 3755 SNP markers with average marker density of 2.94 per cM. Tuber-Cd and Zn concentrations were measured in the segregating population over 2years. QTL mapping identified four loci for tuber-Cd concentration on chromosomes 3, 5, 6, and 7, which explained genetic variance ranging from 5 to 33%, and five loci for tuber-Zn concentration on chromosome 1, 3, 5, and, 6 explaining from 5 to 38% of genetic variance. Among the QTL identified for tuber-Cd concentration, three loci coincided with tuber-Zn concentration. The largest effect QTL for both tuber-Cd and Zn concentration coincided with the maturity locus on chromosome 5 where earliness was associated with increased tuber concentration of both metals. Coincident minor-effect QTL for Cd and Zn sharing the same direction of effect was also found on chromosomes 3 and 6, and these were unrelated to maturity The results indicate partially overlapping genetic control of tuber-Cd and Zn concentration in the cross, involving both maturity-related and non-maturity-related mechanisms.

Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato

Cultivated potatoes (Solanum tuberosum L.), domesticated from wild Solanum species native to the Andes of southern Peru, possess a diverse gene pool representing more than 100 tuber-bearing relatives (Solanum section Petota). A diversity panel of wild species, landraces, and cultivars was sequenced to assess genetic variation within tuber-bearing Solanum and the impact of domestication on genome diversity and identify key loci selected for cultivation in North and South America. Sequence diversity of diploid and tetraploid Stuberosum exceeded any crop resequencing study to date, in part due to expanded wild introgressions following polyploidy that captured alleles outside of their geographic origin. We identified 2,622 genes as under selection, with only 14-16% shared by North American and Andean cultivars, showing that a limited gene set drove early improvement of cultivated potato, while adaptation of upland (Stuberosum group Andigena) and lowland (S. tuberosum groups Chilotanum and Tuberosum) populations targeted distinct loci. Signatures of selection were uncovered in genes controlling carbohydrate metabolism, glycoalkaloid biosynthesis, the shikimate pathway, the cell cycle, and circadian rhythm. Reduced sexual fertility that accompanied the shift to asexual reproduction in cultivars was reflected by signatures of selection in genes regulating pollen development/gametogenesis. Exploration of haplotype diversity at potato's maturity locus (StCDF1) revealed introgression of truncated alleles from wild species, particularly Smicrodontum in long-day-adapted cultivars. This study uncovers a historic role of wild Solanum species in the diversification of long-day-adapted tetraploid potatoes, showing that extant natural populations represent an essential source of untapped adaptive potential.

QTL effects and epistatic interaction for flowering time and branch number in a soybean mapping population of Japanese×Chinese cultivars

Flowering time and branching type are important agronomic traits related to the adaptability and yield of soybean. Molecular bases for major flowering time or maturity loci, E1 to E4, have been identified. However, more flowering time genes in cultivars with different genetic backgrounds are needed to be mapped and cloned for a better understanding of flowering time regulation in soybean. In this study, we developed a population of Japanese cultivar (Toyomusume)×Chinese cultivar (Suinong 10) to map novel quantitative trait locus (QTL) for flowering time and branch number. A genetic linkage map of a F2 population was constructed using 1 306 polymorphic single nucleotide polymorphism (SNP) markers using Illumina SoySNP8k iSelect BeadChip containing 7 189 (SNPs). Two major QTLs at E1 and E9, and two minor QTLs at a novel locus, qFT2_1 and at E3 region were mapped. Using other sets of F2 populations and their derived progenies, the existence of a novel QTL of qFT2_1 was verified. qBR6_1, the major QTL for branch number was mapped to the proximate to the E1 gene, inferring that E1 gene or neighboring genetic factor is significantly contributing to the branch number.

The development and use of a molecular model for soybean maturity groups

BackgroundAchieving appropriate maturity in a target environment is essential to maximizing crop yield potential. In soybean [Glycine max (L.) Merr.], the time to maturity is largely dependent on developmental response to dark periods. Once the critical photoperiod is reached, flowering is initiated and reproductive development proceeds. Therefore, soybean adaptation has been attributed to genetic changes and natural or artificial selection to optimize plant development in specific, narrow latitudinal ranges. In North America, these regions have been classified into twelve maturity groups (MG), with lower MG being shorter season than higher MG. Growing soybean lines not adapted to a particular environment typically results in poor growth and significant yield reductions. The objective of this study was to develop a molecular model for soybean maturity based on the alleles underlying the major maturity loci: E1, E2, and E3.ResultsWe determined the allelic variation and diversity of the E maturity genes in a large collection of soybean landraces, North American ancestors, Chinese cultivars, North American cultivars or expired Plant Variety Protection lines, and private-company lines. The E gene status of accessions in the USDA Soybean Germplasm Collection with SoySNP50K Beadchip data was also predicted. We determined the E allelic combinations needed to adapt soybean to different MGs in the United States (US) and discovered a strong signal of selection for E genotypes released in North America, particularly the US and Canada.ConclusionsThe E gene maturity model proposed will enable plant breeders to more effectively transfer traits into different MGs and increase the overall efficiency of soybean breeding in the US and Canada. The powerful yet simple selection strategy for increasing soybean breeding efficiency can be used alone or to directly enhance genomic prediction/selection schemes. The results also revealed previously unrecognized aspects of artificial selection in soybean imposed by soybean breeders based on geography that highlights the need for plant breeding that is optimized for specific environments.