Semi-dominant Gene Research Articles

The introgression of BjMYB113 from Brassica juncea leads to purple leaf trait in Brassica napus

The purple leaves of Brassica napus are abundant in anthocyanins, which are renowned for their role in conferring distinct colors, stress tolerance, and health benefits, however the genetic basis of this trait in B. napus remains largely unelucidated. Herein, the purple leaf B. napus (PL) exhibited purple pigments in the upper epidermis and a substantial increase in anthocyanin accumulation, particularly of cyanidin, compared to green leaf B. napus (GL). The genetic control of the purple leaf trait was attributed to a semi-dominant gene, pl, which was mapped to the end of chromosome A03. However, sequencing of the fragments amplified by the markers linked to pl indicated that they were all mapped to chromosome B05 from B. juncea. Within this B05 chromosomal segment, the BjMYB113 gene-specific marker showed perfect co-segregation with the purple leaf trait in the F2 population, suggesting that the BjMYB113 introgression from B. juncea was the candidate gene for the purple leaf trait in B. napus. To further verify the function of candidate gene, CRISPR/Cas9 was performed to knock out the BjMYB113 gene in PL. The three myb113 mutants exhibited evident green leaf phenotype, absence of purple pigments in the adaxial epidermis, and a significantly reduced accumulation of anthocyanin compared to PL. Additionally, the genes involved in positive regulatory (TT8), late anthocyanin biosynthesis (DFR, ANS, UFGT), as well as transport genes (TT19) were significantly suppressed in the myb113 mutants, further confirming that BjMYB113 was response for the anthocyanin accumulation in purple leaf B. napus. This study contributes to an advanced understanding of the regulation mechanism of anthocyanin accumulation in B. napus.

BnaC03.BIN2 regulates plant height by affecting the main inflorescence length and first effective branch height in Brassica napus L.

Rapeseed (Brassica napus L.) is one of the main oil crops in the world, and increasing its yield is of great significance for ensuring the safety of edible oil. Presently, improving rapeseed plant architecture is an effective way to increase rapeseed yield with higher planting density. However, the regulatory mechanism of rapeseed plant architecture is poorly understood. In this study, a dwarf rapeseed mutant dwarf08 (df08) is obtained by ethyl methane sulfonate (EMS)-mutagenesis. The decrease in plant height of df08 is mainly caused by the reduction in main inflorescence length and first effective branch height and controlled by a single semi-dominant gene. The hybrid plants (F1) show a semi-dwarf phenotype. Through map-based cloning and transgenic assay, we confirm that the nonsynonymous single nucleotide variant (SNV) (C to T) in BnaC03.BIN2, which is homologous with Arabidopsis (Arabidopsis thaliana) BIN2, is responsible for the dwarfism of df08. BnaC03.BIN2 interacts with BnaBZR1/BES1 and involves in brassinosteroids (BRs) signal transduction. Proline to Leucine substitution in 284 (P284L) enhances the protein stability of BnaC03.bin2-D, disrupts BRs signal transduction and affects the expression of genes regulating cell division, leading to dwarfism of df08. This study provides a new insight for the mechanism of rapeseed plant height regulation and creates an elite germplasm that can be used for genetic improvement of rapeseed architecture.

BnaC01.BIN2, a GSK3-like kinase, modulates plant height and yield potential in Brassica napus.

Using map-based cloning and transgenic transformation, we revealed that glycogen kinase synthase 3-like kinase, BnaC01.BIN2, modulates plant height and yield in rapeseed. The modification of plant height is one of the most important goals in rapeseed breeding. Although several genes that regulate rapeseed plant height have been identified, the genetics mechanisms underlying rapeseed plant height regulation remain poorly understood, and desirable genetic resources for rapeseed ideotype breeding are scarce. Here, we map-based cloned and functionally verified thatthe rapeseed semi-dominant gene, BnDF4, greatly affects rapeseed plant height. Specifically, BnDF4 encodes brassinosteroid(BR)-insensitive 2, a glycogen synthase kinase 3 primarily expressed in the lower internodes to modulate rapeseed plant height by blocking basal internode-cell elongation. Transcriptome data showed that several cell expansion-related genes involving auxin and BRs pathways were significantly downregulated in the semi-dwarf mutant. Heterozygosity in the BnDF4 allele results in small stature with no marked differences in other agronomic traits. Using BnDF4 in the heterozygous condition, the hybrid displayed strong yield heterosis through optimum intermediate plant height. Our results provide a desirable genetic resource for breeding semi-dwarf rapeseed phenotypes and support an effective strategy for breeding rapeseed hybrid varieties with strong yield heterosis.

BnaSD.C3 is a novel major quantitative trait locus affecting semi-dwarf architecture in Brassica napus

Plant height is a key plant architectural trait that affects the seed yield, harvest index and lodging resistance in Brassica napus L., although the genetic mechanisms affecting plant height remain unclear. Here, a semi-dwarf mutant, df34, was obtained by ethyl methanesulphonate-induced mutagenesis. Genetic analysis showed that the semi-dwarf phenotype is controlled by one semi-dominant gene, which was located on chromosome C03 using a bulked segregant analysis coupled with whole-genome sequencing, and this gene was named BnaSD.C3. Then BnaSD.C3 was fine-mapped to a 297.35-kb segment of the “Darmor-bzh” genome, but there was no potential candidate gene for the semi-dwarf trait underlying this interval. Furthermore, the interval was aligned to the Zhongshuang 11 reference genome. Finally, combining structural variation analysis, transcriptome sequencing, phytohormone analyses and gene annotation information, BnaC03G0466900ZS and BnaC03G0478900ZS were determined to be the most likely candidate genes affecting the plant height of df34. This study provides a novel major locus for breeding and new insights into the genetic architecture of plant height in B. napus.

QHD5 encodes an AP2 factor that suppresses rice heading by down-regulating Ehd2 expression

Heading date is crucial for rice reproduction and the geographical expansion of cultivation. We fine-mapped qHD5 and identified LOC_Os05g03040, a gene that encodes an AP2 transcription factor, as the candidate gene of qHD5 in our previous study. In this article, using two near-isogenic lines NIL(BG1) and NIL(XLJ), which were derived from the progeny of the cross between BigGrain1 (BG1) and Xiaolijing (XLJ), we verified that LOC_Os05g03040 represses heading date in rice through genetic complementation and CRISPR/Cas9 gene-editing experiments. Complementary results showed that qHD5 is a semi-dominant gene and that the qHD5XLJ and qHD5BG1 alleles are both functional. The homozygous mutant line generated from knocking out qHD5XLJ in NIL(XLJ) headed earlier than NIL(XLJ) under both short-day and long-day conditions. In addition, the homozygous mutant line of qHD5BG1 in NIL(BG1) also headed slightly earlier than NIL(BG1). All of these results show that qHD5 represses the heading date in rice. Transient expression showed that the qHD5 protein localizes to the nucleus. Transactivation activity assays showed that the C-terminus is the critical site that affects self-activation in qHD5XLJ. qRT-PCR analysis revealed that qHD5 represses flowering by down-regulating Ehd2. qHD5 may have been selected during indica rice domestication.

Integrated genetic mapping and transcriptome analysis reveal the BnaA03.IAA7 protein regulates plant architecture and gibberellin signaling in Brassica napus L.

A novel mutation in the BnaA03.IAA7 protein reduces plant height and enhances gibberellin signaling in Brassica napus L. Rapeseed (Brassica napus) is an excellent and important source for vegetable oil production, but its production is severely affected by lodging. Lodging hinders mechanization and decreases yield, and an ideal solution is semidwarf breeding. Limited by germplasm resources, semidwarf breeding developed slowly in rapeseed. In the current study, a mutant called sdA03 was isolated from EMS-mutagenized lines of Zhongshuang 11 (ZS11). The inheritance analysis showed that phenotypes of sdA03 were controlled by a single semidominant gene. Genetic mapping, RNA-seq and candidate gene analysis identified BnaA03.IAA7 as a candidate gene, and a function test confirmed that the mutated BnaA03.iaa7 regulates plant architecture in a dose-dependent manner. Yeast two-hybrid and transient expression experiments illustrated the P87L substitution in the GWPPV/I degron motif of BnaA03.iaa7 impaired the interaction between BnaA03.IAA7 and TIR1 proteins, and BnaA03.iaa7 prevented ARF from activating the auxin signaling pathway.The gibberellin (GA) content was higher in sdA03 hypocotyls than in those of ZS11. Further expression analysis showed more active gibberellin signaling in hypocotyl and richer expression of GA synthetic genes in root and cotyledon of sdA03 seedlings. Finally, a marker was developed based on the SNP found in BnaA03.iaa7 and used in molecular breeding. The study enriched our understanding of the architectural regulation of rapeseed and provided germplasm resources for breeding.

GmIAA27 Encodes an AUX/IAA Protein Involved in Dwarfing and Multi-Branching in Soybean.

Soybean plant height and branching affect plant architecture and yield potential in soybean. In this study, the mutant dmbn was obtained by treating the cultivar Zhongpin 661 with ethylmethane sulfonate. The dmbn mutant plants were shorter and more branched than the wild type. The genetic analysis showed that the mutant trait was controlled by a semi-dominant gene. The candidate gene was fine-mapped to a 91 kb interval on Chromosome 9 by combining BSA-seq and linkage analysis. Sequence analysis revealed that Glyma.09g193000 encoding an Aux/IAA protein (GmIAA27) was mutated from C to T in the second exon of the coding region, resulting to amino acid substitution of proline to leucine. Overexpression of the mutant type of this gene in Arabidopsis thaliana inhibited apical dominance and promoted lateral branch development. Expression analysis of GmIAA27 and auxin response genes revealed that some GH3 genes were induced. GmIAA27 relies on auxin to interact with TIR1, whereas Gmiaa27 cannot interact with TIR1 owing to the mutation in the degron motif. Identification of this unique gene that controls soybean plant height and branch development provides a basis for investigating the mechanisms regulating soybean plant architecture development.

Increasing floral visitation and hybrid seed production mediated by beauty mark in Gossypium hirsutum.

SummaryHybrid crop varieties have been repeatedly demonstrated to produce significantly higher yields than their parental lines; however, the low efficiency and high cost of hybrid seed production has limited the broad exploitation of heterosis for cotton production. One option for increasing the yield of hybrid seed is to improve pollination efficiency by insect pollinators. Here, we report the molecular cloning and characterization of a semidominant gene, Beauty Mark (BM), which controls purple spot formation at the base of flower petals in the cultivated tetraploid cotton species Gossypium barbadense. BM encodes an R2R3 MYB113 transcription factor, and we demonstrate that GbBM directly targets the promoter of four flavonoid biosynthesis genes to positively regulate petal spot development. Introgression of a GbBM allele into G. hirsutum by marker‐assisted selection restored petal spot formation, which significantly increased the frequency of honeybee visits in G. hirsutum. Moreover, field tests confirmed that cotton seed yield was significantly improved in a three‐line hybrid production system that incorporated the GbBM allele. Our study thus provides a basis for the potentially broad application of this gene in improving the long‐standing problem of low seed production in elite cotton hybrid lines.

Identification and Pleiotropic Effect Analysis of GSE5 on Rice Chalkiness and Grain Shape.

Chalkiness is one of several major restricting factors for the improvement of rice quality. Although many chalkiness-related quantitative trait loci have been mapped, only a small number of genes have been cloned to date. In this study, the candidate gene GSE5 of a major quantitative trait locus (QTL) for rice chalkiness, qDEC5, was identified by map-based cloning. Phenotyping and haplotype analysis of proActin:GSE5 transgenic line, gse5-cr mutant, and 69 rice varieties further confirmed that GSE5 had the pleiotropic effects and regulated both chalkiness and grain shape. Genetic analysis showed GSE5 was a dominant gene for grain length and a semi-dominant gene for grain width and chalkiness. The DNA interval closely linked to GSE5 was introgressed to Zhenshan 97B (ZB) based on molecular marker-assisted selection, and the improved ZB showed lower chalkiness and longer but smaller grains, which showed that GSE5 played an important role in breeding rice varieties with high yield and good quality. Transcriptomics, proteomics, and qRT-PCR analyses showed that thirty-nine genes associated with carbon and protein metabolism are regulated by GSE5 to affect the formation of chalkiness, including some newly discovered genes, such as OsCESA9, OsHSP70, OsTPS8, OsPFK04, OsSTA1, OsERdj3A, etc. The low-chalkiness lines showed higher amino sugar and nucleotide sugar metabolism at 10 days after pollination (DAP), lower carbohydrate metabolism at 15 DAP, and lower protein metabolism at 10 and 15 DAP. With heat shock at 34/30°C, rice chalkiness increased significantly; OsDjC10 and OsSUS3 were upregulated at 6 and 12 DAP, respectively, and OsGSTL2 was downregulated at 12 DAP. Our results identified the function and pleiotropic effects of qDEC5 dissected its genetic characteristics and the expression profiles of the genes affecting the chalkiness formation, and provided a theoretical basis and application value to harmoniously pursue high yield and good quality in rice production.

Fine mapping of the BnaC04.BIL1 gene controlling plant height in Brassica napus L

BackgroundPlant height is an important architecture trait which is a fundamental yield-determining trait in crops. Variety with dwarf or semi-dwarf phenotype is a major objective in the breeding because dwarfing architecture can help to increase harvest index, increase planting density, enhance lodging resistance, and thus be suitable for mechanization harvest. Although some germplasm or genes associated with dwarfing plant type have been carried out. The molecular mechanisms underlying dwarfism in oilseed rape (Brassica napus L.) are poorly understood, restricting the progress of breeding dwarf varieties in this species. Here, we report a new dwarf mutant Bndwarf2 from our B. napus germplasm. We studied its inheritance and mapped the dwarf locus BnDWARF2.ResultsThe inheritance analysis showed that the dwarfism phenotype was controlled by one semi-dominant gene, which was mapped in an interval of 787.88 kb on the C04 chromosome of B. napus by Illumina Brassica 60 K Bead Chip Array. To fine-map BnDWARF2, 318 simple sequence repeat (SSR) primers were designed to uniformly cover the mapping interval. Among them, 15 polymorphic primers that narrowed down the BnDWARF2 locus to 34.62 kb were detected using a F2:3 family population with 889 individuals. Protein sequence analysis showed that only BnaC04.BIL1 (BnaC04g41660D) had two amino acid residues substitutions (Thr187Ser and Gln399His) between ZS11 and Bndwarf2, which encoding a GLYCOGEN SYNTHASE KINASE 3 (GSK3-like). The quantitative real-time PCR (qRT-PCR) analysis showed that the BnaC04.BIL1 gene expressed in all tissues of oilseed rape. Subcellular localization experiment showed that BnaC04.BIL1 was localized in the nucleus in tobacco leaf cells. Genetic transformation experiments confirmed that the BnaC04.BIL1 is responsible for the plant dwarf phenotype in the Bndwarf2 mutants. Overexpression of BnaC04.BIL1 reduced plant height, but also resulted in compact plant architecture.ConclusionsA dominant dwarfing gene, BnaC04.BIL1, encodes an GSK3-like that negatively regulates plant height, was mapped and isolated. Our identification of a distinct gene locus may help to improve lodging resistance in oilseed rape.

Fine mapping and candidate gene analysis of the up locus determining fruit orientation in pepper (Capsicum spp.).

The up locus determining fruit orientation was fine-mapped into a region with a physical length of ~169.51 kb on chromosome P12 in pepper. Capana12g000958, encoding a developmentally regulated G protein 2, was proposed as the strongest candidate via sequence comparison and expression analysis. Fruit orientation is an important horticultural and domesticated trait, which is controlled by a single semi-dominant gene (up) in pepper. However, the gene underlying up locus has not yet been identified. In this study, the previously detected major QTL UP12.1 was firstly verified using a backcross population (n = 225) stem from the cross of BB3 (C. annuum) and its wild relative Chiltepin (C. annuum var. glabriusculum) using BB3 as the recurrent parent. Then, a large BC1F2 population (n = 1827) was used for recombinant screening to delimit the up locus into an interval with ~ 169.51kb in length. Sequence comparison and expression analysis suggested that Capana12g000958, encoding a developmentally regulated G protein 2, was the most likely candidate gene for theup locus. There is no difference within the coding sequences of Capana12g000958 between BB3 and Chiltepin, while a SNP in the upstream of Capana12g000958 showed a complete correlation with the fruit orientation among a panel of 40 diverse pepper inbred lines. These findings will form a basis for gene isolation and reveal of genetic mechanism underlying the fruit orientation domestication in pepper.

Fine mapping of a candidate gene for cool-temperature-induced albinism in ornamental kale

BackgroundThe symptoms of cool-temperature-induced chlorosis (CTIC) are widely existed in higher plants. Although many studies have shown that the genetic mechanism of CTIC is generally controlled by recessive genes in model plants, the dominant inheritance of albinism has not been reported thus far. Here, two CTIC mutants, Red Kamome and White Kamome, were utilized to analyse the inheritance of the albino trait in ornamental kale. The objective of this investigation is to fine-map the target locus and identify the most likely candidate genes for albinism.ResultsGenetic analysis revealed that the albinism in the inner leaves of ornamental kale followed semi-dominant inheritance and was controlled by a single locus in two segregating populations. BSR-seq in combination with linkage analysis was employed to fine-map the causal gene, named AK (Albino Kale), to an approximate 60 kb interval on chromosome C03. Transcriptome data from two extreme pools indicated that the differentially expressed gene of Bol015404, which encodes a cytochrome P450 protein, was the candidate gene. The Bol015404 gene was demonstrated to be upregulated in the albino leaves of ornamental kale by qPCR. Additionally, the critical temperature for the albinism was determined between 10 °C and 16 °C by gradient test.ConclusionsUsing two independent segregating populations, the albino mutants were shown to be controlled by one semi-dominant gene, AK, in ornamental kale. The Bol015404 gene was co-segregated with albinism phenotypes, suggesting this unknown function P450 gene as the most likely candidate gene. The albino trait appeared caused by the low temperatures rather than photoperiod. Our results lay a solid foundation on the genetic control of albinism in ornamental kale.

The dihydroflavonol 4-reductase BoDFR1 drives anthocyanin accumulation in pink-leaved ornamental kale.

Overexpression and virus-induced gene silencing verified BoDFR1 conferred the anthocyanin accumulation in pink-leaved ornamental kale. Leaf color is an essential trait in the important horticultural biennial plant ornamental kale (Brassica oleracea var. acephala). The identity of the gene conferring this striking trait and its mode of inheritance are topics of debate. Based on an analysis of F1, F2, BC1P1, and BC1P2 ornamental kale populations derived from a cross between a pink-leaved P28 and white-leaved D10 line, we determined that the pink leaf trait is controlled by a semi-dominant gene. We cloned two genes potentially involved in anthocyanin biosynthesis in ornamental kale: Bo9g058630 and Bo6g100940. Based on their variation in sequence, we speculated that Bo9g058630, encoding the kale dihydroflavonol-4 reductase (BoDFR1) enzyme, plays a critical role in the development of the pink leaf trait. Indeed, an InDel marker specific for BoDFR1 completely co-segregated with the pink leaf trait in our F2 population. We then generated the 35Spro: DFR-GUS overexpression vector, which we transformed into D10. Overexpression of BoDFR1 indeed restored some anthocyanin accumulation in this white-leaved parental line. In addition, we targeted BoDFR1 in P28 using virus-induced gene silencing. Again, silencing of BoDFR1 resulted in a substantial decrease in anthocyanin accumulation. This work lays the foundation for further exploration of the mechanism underlying anthocyanin accumulation in pink-leaved ornamental kale.

Fine-mapping and transcriptome analysis of a candidate gene controlling plant height in Brassica napus L.

BackgroundBrassica napus provides approximately 13–16% of global vegetable oil for human consumption and biodiesel production. Plant height (PH) is a key trait that affects plant architecture, seed yield and harvest index. However, the genetic mechanism of PH in B. napus is poorly understood.ResultsA dwarf mutant df59 was isolated from a large-scale screening of an ethyl methanesulphonate-mutagenized rapeseed variety Ningyou 18. A genetic analysis showed that the dwarfism phenotype was controlled by one semi-dominant gene, which was mapped on C9 chromosome by quantitative trait loci sequencing analysis and designated as BnaDwf.C9. To fine-map BnaDwf.C9, two F2 populations were constructed from crosses between conventional rapeseed cultivars (Zhongshuang 11 and Holly) and df59. BnaDwf.C9 was fine-mapped to the region between single-nucleotide polymorphism (SNP) markers M14 and M4, corresponding to a 120.87-kb interval of the B. napus ‘Darmor-bzh’ genome. Within this interval, seven, eight and nine annotated or predicted genes were identified in “Darmor-bzh”, “Ningyou 7” and “Zhongshuang 11” reference genomes, respectively. In addition, a comparative transcriptome analysis was performed using stem tips from Ningyou 18 and df59 at the stem elongation stage. In total, 3995 differentially expressed genes (DEGs) were identified. Among them, 118 DEGs were clustered in plant hormone-related signal transduction pathways, including 81 DEGs were enriched in auxin signal transduction. Combining the results of fine-mapping and transcriptome analyses, BnaC09g20450D was considered a candidate gene for BnaDwf.C9, which contains a SNP that co-segregated in 4746 individuals. Finally, a PCR-based marker was developed based on the SNP in BnaC09g20450D.ConclusionsThe combination of quantitative trait loci sequencing, fine-mapping and genome-wide transcriptomic analysis revealed one candidate gene located within the confidence interval of 120.87-kb region. This study provides a new genetic resource for semi-dwarf breeding and new insights into understanding the genetic architecture of PH in B. napus.

Fine mapping and identification of the leaf shape gene BoFL in ornamental kale.

BoFL, a candidate gene conferring the feathered-leaved trait in ornamental kale, is located in a 374.532-kb region on chromosome C9. Leaf shape is an important economic trait in ornamental kale (Brassica oleracea var. acephala). Identifying the genes that influence leaf shape would provide insight into the mechanism underlying leaf development. In this study, we constructed F1, F2, BC1P1, BC1P2, and F2:3 populations from a cross between a feathered-leaved inbred line, F0819, and a smooth-leaved inbred line, S0835, of ornamental kale. Genetic analysis showed that the feathered-leaved trait was controlled by a semi-dominant gene, BoFL. Using bulked segregant analysis sequencing, we mapped the BoFL gene to a 4.17-Mb interval on chromosome C9. Next, we narrowed down the candidate region to 374.532-kb by fine-scale mapping between the two flanking markers INDEL940 and INDEL5443. We identified 38 genes in the candidate region, among which only Bo9g184610 showed significant variation in expression level between the two parental lines. Sequencing of the gene in the parental lines identified three single-nucleotide polymorphism (SNP) differences, containing two nonsynonymous and one synonymous SNPs, which resulted in coding variations of an aspartate and a phenylalanine residue in F0819, but an alanine and a leucine residue in S0835. A cleaved amplified polymorphic sequence (CAPS) marker, CAPS4610, corresponding to the first nonsynonymous SNP co-segregated with the leaf shape trait. We thus speculated that the gene conferring the feathered-leaved trait is BoALG10, a homolog of ALG10, which encodes an alpha-1,2-glucosyltransferase in Arabidopsis thaliana. This work will be useful for understanding the mechanism of leaf development and provides important information for the breeding of kale with novel leaf shapes.

The semidominant mutation w5 impairs epicuticular wax deposition in common wheat (Triticum aestivum L.).

The semidominant EMS-induced mutant w5 affects epicuticular wax deposition and mapped to an approximately 194-kb region on chromosome 7DL. Epicuticular wax is responsible for the glaucous appearance of plants and protects against many biotic and abiotic stresses. In wheat (Triticum aestivum L.), β-diketone is a major component of epicuticular wax in adult plants and contributes to the glaucousness of the aerial organs. In the present study, we identified an ethyl methanesulfonate-induced epicuticular wax-deficient mutant from the elite wheat cultivar Jimai22. Compared to wild-type Jimai22, the mutant lacked β-diketone and failed to form the glaucous coating on all aerial organs. The mutant also had significantly increased in cuticle permeability, based on water loss and chlorophyll efflux. Genetic analysis indicated that the mutant phenotype is controlled by a single, semidominant gene on the long arm of chromosome 7D, which was not allelic to the known wax gene loci W1-W4, and was therefore designated W5. W5 was finely mapped to an ~ 194-kb region (flanked by the molecular markers SSR2 and STARP11) that harbored four annotated genes according to the reference genome of Chinese Spring (RefSeq v1.0). Collectively, these data will broaden the knowledge of the genetic basis underlying epicuticular wax deposition in wheat.

Inheritance of pre-emergent metribuzin tolerance and putative gene discovery through high-throughput SNP array in wheat (Triticum aestivum L.)

BackgroundHerbicide tolerance is an important trait that allows effective weed management in wheat crops in dryland farming. Genetic knowledge of metribuzin tolerance in wheat is needed to develop new cultivars for the industry. Here, we investigated gene effects for metribuzin tolerance in nine crosses of wheat by partitioning the means and variances of six basic generations from each cross into their genetic components to assess the gene action governing the inheritance of this trait. Metribuzin tolerance was measured by a visual senescence score 21 days after treatment. The wheat 90 K iSelect SNP genotyping assay was used to identify the distribution of alleles at SNP sites in tolerant and susceptible groups.ResultsThe scaling and joint-scaling tests indicated that the inheritance of metribuzin tolerance in wheat was adequately described by the additive-dominance model, with additive gene action the most significant factor for tolerance. The potence ratio for all the crosses ranged between − 1 and + 1 for senescence under metribuzin-treated conditions indicating a semi-dominant gene action in the inheritance of metribuzin tolerance in wheat. The number of segregating genes governing metribuzin tolerance was estimated between 3 and 15. The consistent high heritability range (0.82 to 0.92) in F5–7 generations of Chuan Mai 25 (tolerant) × Ritchie (susceptible) cross indicated a significant contribution of additive genetic effects to metribuzin tolerance in wheat. Several genes related to photosynthesis (e.g. photosynthesis system II assembly factor YCF48), metabolic detoxification of xenobiotics and cell growth and development (cytochrome P450, glutathione S-transferase, glycosyltransferase, ATP-binding cassette transporters and glutathione peroxidase) were identified on different chromosomes (2A, 2D, 3B, 4A, 4B, 7A, 7B, 7D) governing metribuzin tolerance.ConclusionsThe simple additive–dominance gene effects for metribuzin tolerance will help breeders to select tolerant lines in early generations and the identified genes may guide the development of functional markers for metribuzin tolerance.

Whole-Genome Sequencing Identifies a Rice Grain Shape Mutant, gs9\u20131

BackgroundBreeding for genes controlling key agronomic traits is an important goal of rice genetic improvement. To gain insight into genes controlling grain morphology, we screened M3 plants derived from 1,000 whole-genome sequenced (WGS) M2 Kitaake mutants to identify lines with altered grain size.ResultsIn this study, we isolated a mutant, named fast-neutron (FN) 60–4, which exhibits a significant reduction in grain size. We crossed FN60–4 with the parental line Kitaake and analyzed the resulting backcross population. Segregation analysis of 113 lines from the BC2F2 population revealed that the mutant phenotype is controlled by a single semi-dominant locus. Mutant FN60–4 is reduced 20% in plant height and 8.8% in 1000-grain weight compared with Kitaake. FN60–4 also exhibits an 8% reduction in cell number and a 9% reduction in cell length along the vertical axis of the glume. We carried out whole-genome sequencing of DNA pools extracted from segregants with long grains or short grains, and revealed that one gene, LOC_Os09g02650, cosegregated with the grain size phenotype in the BC1F2 and BC2F2 populations. This mutant allele was named grain shape 9–1 (gs9–1). gs9–1 carries a 3-bp deletion that affects two amino acids. This locus is a new allele of the BC12/GDD1/MTD1 gene that encodes a kinesin-like protein involved in cell-cycle progression, cellulose microfibril deposition and gibberellic acid (GA) biosynthesis. The GA biosynthesis-related gene KO2 is down-regulated in gs9–1. The dwarf phenotype of gs9–1 can be rescued by adding exogenous GA3. In contrast to the phenotypes for the other alleles, the gs9–1 is less severe, consistent with the nature of the mutation, which does not disrupt the open reading frame as observed for the other alleles.ConclusionsIn this study, we isolated a mutant, which exhibits altered grain shape and identified the mutated gene, gs9–1. Our study reveals that gs9–1 is a semi-dominant gene that carries a two-amino acid mutation. gs9–1 is allelic to the BC12/GDD1/MTD1 gene involved in GA biosynthesis. These results demonstrate the efficiency and convenience of cloning genes from the whole-genome sequenced Kitaake mutant population to advance investigations into genes controlling key agronomic traits in rice.

Molecular mapping and candidate gene analysis of the semi-dominant gene Vestigial glume1 in maize

The glume is an organ of the maize spikelet and plays important roles in anther and kernel development. Vestigial glume1 (Vg1) is a classic mutant associated with ligule and glume development. Here we report the phenotypic characterization, fine mapping, and candidate gene analysis of the Vg1 mutant. Vg1 is a semi-dominant and pleiotropic gene, and also affects plant height, ear height, and tassel length. Vg1 ligule degeneration begins at the first leaf, and the Vg1 tassel and ear can be distinguished from those of wild-type plants when their lengths reach respectively 55 mm and 51 mm. Using a BC3 mapping population of 11,445 plants, we delimited the Vg1 functional site to an interval of 7.4 kb, flanked by the markers InDelLM and CRM6. A putative cyclopropane fatty-acid synthase gene (ZmCPA-FAS1) was hypothesized to underlie the mutant phenotype. We detected a Helitron insertion in the sixth intron of ZmCPA-FAS1. Its presence caused abnormal alternative splicing of ZmCPA-FAS1 that conferred new characteristics on the Vg1 mutant. These findings are a basis for further discovery of the molecular mechanism underlying glume development and a potential guide for maize breeding of small-glume varieties, especially sweet corn breeding.

Genetic mapping and expressivity of a wheat multi-pistil gene in mutant 12TP

We identified a wheat (Triticum aestivum L.) multi-pistil mutant from an F2 breeding population in 2012, named 12TP (three pistils in one floret). Genetic analysis showed that one dominant gene locus controlled the multi-pistil trait. Using homozygous normal and multi-pistil lines (near-isogenic lines; NILs) derived from the original mutant 12TP, a simple sequence repeat (SSR) marker assay located the 12TP locus on chromosome arm 2DL. Four SSR markers were linked to 12TP and their order was Xcfd233→Xcfd62-12TP→Xwmc41→Xcfd168 at 15.85, 10.47, 2.89, and 10.37 cM, respectively. The average genetic expressivity of the trait ‘three pistils in one floret’ was more than 98% in seven homozygous 12TP lines; however, the average genetic expressivity in heterozygous F1 plants was about 49%. Thus, the 12TP is a semi-dominant gene locus, which differ from all previously reported multi-pistil mutants. Mutant 12TP is a new useful germplasm for study of wheat floral development and for breeding of high yield wheat.