Dominant Locus Research Articles

Natural variation at the cotton HIC locus increases trichome density and enhances resistance to aphids.

Plant trichomes are an excellent model for studying cell differentiation and development, providing crucial defenses against biotic and abiotic stresses. There is a well-established inverse relationship between trichome density and aphid prevalence, indicating that higher trichome density leads to reduced aphid infestations. Here we present the cloning and characterization of a dominant quantitative trait locus, HIC (hirsute cotton), which significantly enhances cotton trichome density. This enhancement leads to markedly improved resistance against cotton aphids. The HIC encodes an HD-ZIP IV transcriptional activator, crucial for trichome initiation. Overexpression of HIC leads to a substantial increase in trichome density, while knockdown of HIC results in a marked decrease in density, confirming its role in trichome regulation. We identified a variant in the HIC promoter (-810 bp A to C) that increases transcription of HIC and trichome density in hirsute cotton compared with Gossypium hirsutum cultivars with fewer or no trichomes. Interestingly, although the -810 variant in the HIC promoter is the same in G. barbadense and hirsute cotton, the presence of a copia-like retrotransposon insertion in the coding region of HIC in G. barbadense causes premature transcription termination. Further analysis revealed that HIC positively regulates trichome density by directly targeting the EXPANSIN A2 gene, which is involved in cell wall development. Taken together, our results underscore the pivotal function of HIC as a primary regulator during the initial phases of trichome formation, and its prospective utility in enhancing aphid resistance in superior cotton cultivars via selective breeding.

Fertility restorer gene CaRf and PepperSNP50K provide a promising breeding system for hybrid pepper.

Cytoplasmic male sterility (CMS) is pivotal in plant breeding and widely employed in various crop hybrids, including pepper. However, the functional validation of the restorer of fertility (Rf) gene in pepper has been lacking until now. This study identifies and characterizes CaRf, a single dominant locus crucial for restoring CMS in the pepper strong recovery inbred line Zhangshugang. The CaRf gene encodes a mitochondria-targeted pentatricopeptide repeat protein, validated through the induction of male sterility upon its silencing in hybrid F1 plants. To enhance pepper breeding efficiency, 176 important pepper breeding parent materials were resequenced, and a PepperSNP50K liquid-phase breeding chip was developed, comprising 51 172 markers. Integration of CaRf functional characterization and PepperSNP50K facilitated the development of a high-quality red pepper hybrid. These findings provide significant insights and practical strategies for advancing molecular-designed breeding in peppers.

Mapping and transcriptomic profiling reveal that the KNAT6 gene is involved in the dark green peel colour of mature pumpkin fruit (Cucurbita maxima L.).

We identified a 580bp deletion of CmaKNAT6 coding region influences peel colour of mature Cucurbita maxima fruit. Peel colour is an important agronomic characteristic affecting commodity quality in Cucurbit plants. Genetic mapping of fruit peel colour promotes molecular breeding and provides an important basis for understanding the regulatory mechanism in Cucurbit plants. In the present study, the Cucurbita maxima inbred line '9-6' which has a grey peel colour and 'U3-3-44' which has a dark green peel colour in the mature fruit stage, were used as plant materials. At 5-40days after pollination (DAP), the contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoids in the 'U3-3-44' peels were significantly greater than those in the '9-6' peels. In the epicarp of the '9-6' mature fruit, the presence of nonpigmented cell layers and few chloroplasts in each cell in the pigmented layers were observed. Six generations derived by crossing '9-6' and 'U3-3-44' were constructed, and the dark green peel was found to be controlled by a single dominant locus, which was named CmaMg (mature green peel). Through bulked-segregant analysis sequencing (BSA-seq) and insertion-deletion (InDel) markers, CmaMg was mapped to a region of approximately 449.51kb on chromosome 11 using 177 F2 individuals. Additionally, 1703 F2 plants were used for fine mapping to compress the candidate interval to a region of 32.34kb. Five coding genes were in this region, and CmaCh11G000900 was identified as a promising candidate gene according to the reported function, sequence alignment, and expression analyses. CmaCh11G000900 (CmaKNAT6) encodes the homeobox protein knotted-1-like 6 and contains 4 conserved domains. CmaKNAT6 of '9-6' had a 580bp deletion, leading to premature transcriptional termination. The expression of CmaKNAT6 tended to increase sharply during the early fruit development stage but decrease gradually during the late period of fruit development. Allelic diversity analysis of pumpkin germplasm resources indicated that the 580bp deletion in the of CmaKNAT6 coding region was associated with peel colour. Subcellular localization analysis indicated that CmaKNAT6 is a nuclear protein. Transcriptomic analysis of the inbred lines '9-6' and 'U3-3-44' indicated that genes involved in chlorophyll biosynthesis were more enriched in 'U3-3-44' than in '9-6'. Additionally, the expression of transcription factor genes that positively regulate chlorophyll synthesis and light signal transduction pathways was upregulated in 'U3-3-44'. These results lay a foundation for further studies on the genetic mechanism underlying peel colour and for optimizing peel colour-based breeding strategies for C. maxima.

Structural complexity of the white flower locus in Chrysanthemum

ABSTRACT The white flower trait in Chrysanthemum is attributed to the carotenoid cleavage dioxygenase 4a gene (CCD4a), a key domestication gene that contributed to generation of various flower colours in modern chrysanthemum cultivars. This trait is believed to be controlled by a single dominant locus. We studied the structure of this CCD4a locus utilising the whole genome sequence information of Chrysanthemum makinoi, a diploid white flower species, and found six homologous sequences of CCD4a, two of which being functional, and arranged in tandem in a 586-kb region on Chromosome 7. A qPCR analysis disclosed that white flower Chrysanthemum species possess at least two and as many as eight copies of CCD4a homologous sequences per monoploid genome, indicating high polymorphism of the CCD4a region. A detailed analysis of the structural diversity of the CCD4a region in Chrysanthemum could provide significant insights into the domestication trajectory of the cultivated chrysanthemum.

Fine mapping and transcriptome profiling reveal CpAPRR2 to modulate immature fruit rind color formation in zucchini (Cucurbita pepo).

A large fragment deletion of CpAPRR2, encoding a two-component response regulator-like protein, which influences immature white rind color formation in zucchini (Cucurbita pepo). Fruit rind color is an important agronomic trait that affects commodity quality and consumer choice in zucchini (Cucurbita pepo). However, the molecular mechanism controlling rind color is unclear. We characterized two zucchini inbred lines: '19' (dark green rind) and '113' (white rind). Genetic analysis revealed white immature fruit rind color to be controlled by a dominant locus (CpW). Combining bulked segregant analysis sequencing (BSA-seq) and Kompetitive Allele-Specific PCR (KASP) markers, we mapped the CpW locus to a 100.4kb region on chromosome 5 and then narrow down the candidate region to 37.5kb using linkage analysis of 532 BC1 and 1613 F2 individuals, including 6 coding genes. Among them, Cp4.1LG05g02070 (CpAPRR2), encoding a two-component response regulator-like protein, was regarded to be a promising candidate gene. The expression level of CpAPRR2 in dark green rind was significantly higher than that in white rind and was induced by light. A deletion of 2227bp at the 5' end of CpAPRR2 in '113' might explain the white phenotype. Further analysis of allelic diversity in zucchini germplasm resources revealed rind color to be associated with the deletion of CpAPRR2. Subcellular localization analysis indicated that CpAPRR2 was a nuclear protein. Transcriptome analysis using near-isogenic lines with dark green (DG) and white (W) rind indicated that genes involved in photosynthesis and porphyrin metabolism pathways were enriched in DG compared with W. Additionally, chlorophyll synthesis-related genes were upregulated in DG. These results identify mechanisms of zucchini rind color and provide genetic resources for breeding.

Different control of resistance to two Colletotrichum orbiculare pathogenic races 0 and 1 in cucumber (Cucumis sativus L.).

Quantitative trait locus analysis identified independent novel loci in cucumbers responsible for resistance to races 0 and 1 of the anthracnose fungal pathogen Colletotrichum orbiculare. Cucumbers have been reported to be vulnerable to Colletotrichum orbiculare, causing anthracnose disease with significant yield loss under favorable conditions. The deployment of a single recessive Cssgr gene in cucumber breeding for anthracnose resistance was effective until a recent report on high-virulent strains infecting cucumbers in Japan conquering the resistance. QTL mapping was conducted to identify the resistance loci in the cucumber accession Ban Kyuri (G100) against C. orbiculare strains 104-T and CcM-1 of pathogenic races 0 and 1, respectively. A single dominant locus An5 was detected in the disease resistance hotspot on chromosome 5 for resistance to 104-T. Resistance to CcM-1 was governed by three loci with additive effects located on chromosomes 2 (An2) and 1 (An1.1 and An1.2). Molecular markers were developed based on variant calling between the corresponding QTL regions in the de novo assembly of the G100 genome and the publicly available cucumber genomes. Multiple backcrossed populations were deployed to fine-map An5 locus and narrow the region to approximately 222 kbp. Accumulation of An2 and An1.1 alleles displayed an adequate resistance to CcM-1 strain. This study provides functional molecular markers for pyramiding resistance loci that confer sufficient resistance against anthracnose in cucumbers.

Identification and transfer of resistance to Fusarium head blight from Elymus repens chromosome arm 7StL into wheat

Fusarium head blight (FHB), mainly caused by Fusarium graminearum (Fg), is one of the most devastating fungal diseases in wheat production worldwide. Elymus repens (2n=6x=42, StStStStHH) is a wild relative of wheat with many biotic and abiotic stress resistance traits. To transfer and apply the wild germplasm's resistance gene (s) for wheat breeding, we identified a new translocation line K140-7 with high resistance to FHB, developed from the derivative progenies of E. repens crossed with common wheat cultivars. Cytogenetic analyses based on genomic in situ hybridization (GISH), non-denaturing fluorescence in situ hybridization (ND-FISH), oligonucleotide-FISH painting (Oligo-FISH painting), and single-gene FISH revealed that K140-7 had 40 wheat chromosomes and two 7DS·7StL translocated chromosomes. Wheat 55K SNP array analysis confirmed that the translocated breakpoint (340.8~342.5 Mb) was close to the centromere region of chromosome 7D (336.3~341.7 Mb), supporting the 7DS·7StL translocation event. Based on the diploid reference St genome of Pseudoroegneria libanotica, we developed 21 simple sequence repeats (SSR) markers, specific for chromosome arm 7StL. Genotyping and phenotyping analysis of the 7DS·7StL translocation in different wheat backgrounds demonstrated that the chromosome arm 7StL confers FHB resistance and possesses the dominant FHB resistance locus (s) named QFhb.Er-7StL. We further transferred QFhb.Er-7StL into three different wheat cultivars, their second 7DS·7StL translocation line-generations showed improved agronomic traits, representing new germplasms that could be used in wheat FHB-resistant breeding programs.

Delayed resonator with multiple distributed delays – Considering and optimizing the inherent loop delay

We generalize the distributed delayed resonator (DDR) concept by incorporating the previously unutilized but inevitable feedback loop delay, thus creating a so-called multiple-delay distributed delayed resonator (MD-DDR) for complete vibration suppression. The necessary parameter tuning and control stability analysis become more involved but remain analytically solvable. Particularly, we take the operability of control parameters imposed by hardware as an explicit condition for parameter tuning and show that the loop delay (even if it is small) can lead to incomplete vibration suppression and, counter-intuitively, even no suppression if the excitation frequency exceeds a threshold value. On the other hand, such negative effects are neutralized by correcting control parameters. The loop delay is then intentionally augmented to seek enhanced performance, yielding a considerably extended operable frequency band for the desired complete vibration suppression. Furthermore, it is optimized to expedite response speed by achieving the leftmost placement of the dominant (i.e., the rightmost) characteristic root. Instead of applying a brute-force sweeping procedure as in the previous works, we analyze the dominant root locus and seek if the jump phenomenon occurs to conduct exact optimization at a low computational cost. Finally, extensive comparisons using actual experimental parameters are performed to explore various effects of the loop delay on vibration suppression and the benefits of the proposed MD-DDR in handling such issues over the conventional DDR that treats a single delay. This study fully exploits the strength of the distributed delayed control logic, moving the DDR concept closer to real applications and aiming to establish a broader design and analysis framework for the delayed resonator from a multiple-delay perspective.

Differential expression of ASIP transcripts reveals genetic mechanism underpinning black-tail independence from body plumage in yellow-bodied chickens.

The genetic foundation of chicken body plumage color has been extensively studied. However, little attention has been paid to the inheritance patterns and molecular mechanisms underlying the formation of distal feather colors (tail and wingtip). Differences in these colors are common; for example, the Chinese Huiyang Beard chicken has black tail feathers, but yellow body plumage. Here, the hybrid offspring of Huiyang Beard and White Leghorn chickens were used to study the inheritance patterns of tail-feather color. The expression levels of pigment genes in differently colored feather follicles were analyzed using quantitative real-time PCR. The results showed that genetic regulation of tail-feather color was independent of body-plumage color. The Dominant White locus inhibited eumelanin synthesis in tail feathers without affecting the formation of yellow body plumage, whereas the Silver locus had the opposite effect. The expression of agouti signaling protein (ASIP) gene class 1 transcripts was significantly lower in black tail-feather follicles than in yellow body follicles, whereas tyrosinase-related protein 1 (TYRP1) gene expression was significantly higher in black tail feathers. These differentially expressed genes were confirmed to exert an effect on eumelanin and pheomelanin formation in feathers, thus influencing the regulation of chicken tail-feather color. In conclusion, this study lays the foundation for further research on the genetic mechanisms of regional differences in feather color, contributing to a better understanding of plumage pigmentation in chickens.

Recent Advances in Natural Deastringency and Genetic Improvement of Chinese PCNA Persimmon (Diospyros kaki)

Persimmon (Diospyros kaki) is a worldwide fruit cultivated mainly in the East Asia, Mediterranean, Caucasus, Latin America, and Oceania regions. This fruit contains abundant proanthocyanidins (PAs, also called condensed tannins), whose biosynthesis is the main cause of fruit astringency. As the original centre and top producing country, China has discovered a unique type with desirable natural deastringency, the Chinese pollination-constant non-astringent (C-PCNA) persimmon. Studies have revealed that the C-PCNA trait is controlled by a single and dominant locus, which differs from that of another type, the Japanese PCNA type, with recessive loci. In the C-PCNA type, accumulating evidence has shown that the astringency removal process involves two pathways (“dilution effect” and “coagulation effect”). Moreover, molecular marker-assisted selection (MAS) for the natural deastringency trait locus in C-PCNA has been used to test the non-astringency/astringency trait of hybrid offspring at the seedling stage. Importantly, persimmon can bear male flowers, female flowers, and perfect flowers, but sex-linked MAS has been developed for female-only persimmon. This sex-linked MAS, together with astringency-linked MAS and embryo rescue technology, may even shorten the conventional cross-breeding period of about 2–3 years. In addition, recently studies have established a stable genetic transformation system for persimmon transgenic improvement. Despite these efforts, how synthetic PAs and metabolism pathways lead to a deastringent trait remains unclear for persimmon. Thus, our review summarizes the latest research progress on the natural deastringency mechanism in C-PCNA, and we provide a new viewpoint for the genetic improvement of persimmon breeding in China.

A 1-bp deletion in the MC04g1399 is highly associated with failure to produce fruit wart in bitter gourd (Momordica charantia L.)

Fruit wart is an important appearance trait influencing consumer preferences of bitter gourd. The molecular genetic mechanisms underlying fruit wart formation in bitter gourd are largely unknown. In this study, genetic analysis based on four generations showed that fruit wart formation in bitter gourd was controlled by a single dominant locus named as Fwa. The Fwa locus was initially mapped into a 4.82 Mb region on pseudochromosome 4 by BSA-seq analysis and subsequently narrowed down to a 286.30 kb region by linkage analysis. A large F2 population consisting of 2 360 individuals was used to screen recombinants, and the Fwa locus was finally fine mapped into a 22.70 kb region harboring four protein-coding genes through recombination analysis. MC04g1399, encoding an epidermal patterning factor 2-like protein, was proposed as the best candidate gene for Fwa via sequence variation and expression analysis. In addition, a 1-bp insertion and deletion (InDel) variation within MC04g1399 was converted to a cleaved amplified polymorphic sequence (CAPS) marker that could precisely distinguish between the warty and non-warty types with an accuracy rate of 100 % among a wide panel of 126 bitter gourd germplasm resources. Our results not only provide a scientific basis for deciphering the molecular mechanisms underlying fruit wart formation but also provide a powerful tool for efficient genetic improvement of fruit wart via marker-assisted selection.

A butterfly egg-killing hypersensitive response in Brassica nigra is controlled by a single locus, PEK, containing a cluster of TIR-NBS-LRR receptor genes.

Knowledge of plant recognition of insects is largely limited to a few resistance (R) genes against sap-sucking insects. Hypersensitive response (HR) characterizes monogenic plant traits relying on R genes in several pathosystems. HR-like cell death can be triggered by eggs of cabbage white butterflies (Pieris spp.), pests of cabbage crops (Brassica spp.), reducing egg survival and representing an effective plant resistance trait before feeding damage occurs. Here, we performed genetic mapping of HR-like cell death induced by Pieris brassicae eggs in the black mustard Brassica nigra (B. nigra). We show that HR-like cell death segregates as a Mendelian trait and identified a single dominant locus on chromosome B3, named PEK (Pieris egg- killing). Eleven genes are located in an approximately 50 kb region, including a cluster of genes encoding intracellular TIR-NBS-LRR (TNL) receptor proteins. The PEK locus is highly polymorphic between the parental accessions of our mapping populations and among B. nigra reference genomes. Our study is the first one to identify a single locus potentially involved in HR-like cell death induced by insect eggs in B. nigra. Further fine-mapping, comparative genomicsand validation of the PEK locus will shed light on the role of these TNL receptors in egg-killing HR.

Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis

Exploitation of crop heterosis is crucial for increasing global agriculture production. However, the quantitative genomic analysis of heterosis was lacking, and there is currently no effective prediction tool to optimize cross-combinations. Here 2,839 rice hybrid cultivars and 9,839 segregation individuals were resequenced and phenotyped. Our findings demonstrated that indica–indica hybrid-improving breeding was a process that broadened genetic resources, pyramided breeding-favorable alleles through combinatorial selection and collaboratively improved both parents by eliminating the inferior alleles at negative dominant loci. Furthermore, we revealed that widespread genetic complementarity contributed to indica–japonica intersubspecific heterosis in yield traits, with dominance effect loci making a greater contribution to phenotypic variance than overdominance effect loci. On the basis of the comprehensive dataset, a genomic model applicable to diverse rice varieties was developed and optimized to predict the performance of hybrid combinations. Our data offer a valuable resource for advancing the understanding and facilitating the utilization of heterosis in rice.

A single dominant locus restricts retrovirus replication in YBR/Ei mice.

Differential responses to viral infections are influenced by the genetic makeup of the host. Studies of resistance to retroviruses in human populations are complicated due to the inability to conduct proof-of-principle studies. Inbred mouse lines, which have a range of susceptible phenotypes to retroviruses, are an ideal tool to identify and characterize mechanisms of resistance and define their genetic underpinnings. YBR/Ei mice become infected with Mouse Mammary Tumor Virus, a mucosally transmitted murine retrovirus, but eliminate the virus from their pedigrees. Virus elimination correlates with a lack of virus-specific neonatal oral tolerance, which is a major mechanism for blocking the anti-virus response in susceptible mice. Virus control is unrelated to virus-neutralizing antibodies, cytotoxic CD8+ T cells, NK cells, and NK T cells, which are the best characterized mechanisms of resistance to retroviruses. We identified a single, dominant locus that controls the resistance mechanism, which we provisionally named attenuation of virus titers (Avt) and mapped to the distal region of chromosome 18. IMPORTANCE Elucidation of the mechanism that mediates resistance to retroviruses is of fundamental importance to human health, as it will ultimately lead to knowledge of the genetic differences among individuals in susceptibility to microbial infections.

Promoter variations in a homeobox gene, BrLMI1, contribute to leaf lobe formation in Brassica rapa ssp. chinensis Makino.

Key message BrLMI1 is a positive regulatory factor of leaf lobe formation in non-heading Chinese cabbage, and cis-regulatory variations lead to the phenotype of lobed or entire leaf margins.Abstract Leaves are the main consumed organ in leafy non-heading Chinese cabbage (Brassica rapa L. ssp. chinensis Makino), and the shape of the leaves is an important economic trait. However, the molecular regulatory mechanism underlying the lobed-leaf trait in non-heading Chinese cabbage remains unclear. Here, we identified a stable incompletely dominant major locus, qLLA10, for lobed leaf formation in non-heading Chinese cabbage. Based on map-based cloning strategies, BrLMI1, a LATE MERISTEM IDENTITY1 (LMI1)-like gene, was predicted as the candidate gene for qLLA10. Genotyping analysis showed that promoter variations of BrLMI1 in the two parents are responsible for elevating the expression in the lobed-leaf parent and ultimately causing the difference in leaf shape between the two parents, and the promoter activity of BrLMI1 was significantly affected by the promoter variations. BrLMI1 was exclusively localized in the nucleus and expressed mainly at the tip of each lobe. Leaf lobe development was perturbed in BrLMI1-silenced plants produced by virus-induced gene silencing assays, and ectopic overexpression of BrLMI1 in Arabidopsis led to deeply lobed leaves never seen in the wild type, which indicates that BrLMI1 is required for leaf lobe formation in non-heading Chinese cabbage. These findings suggested that BrLMI1 is a positive regulatory factor of leaf lobe formation in non-heading Chinese cabbage and that cis-regulatory variations lead to the phenotype of lobed or entire leaf margins, thus providing a theoretical basis for unraveling the molecular mechanism underlying the lobed leaf phenotype in Brassica crops.

Insights into the pathophysiology of DFNA44 hearing loss associated with CCDC50 frameshift variants.

Non-syndromic sensorineural hearing loss (SNHL) is the most common sensory disorder, and it presents a high genetic heterogeneity. As part of our clinical genetic studies, we ascertained a novel mutation in CCDC50 (c.828_858del, p.(Asp276Glufs*40)) segregating with the hearing impairment in a Spanish family with autosomal dominant DFNA44 SNHL that is predicted to disrupt the protein function. To gain insight into the mechanism behind DFNA44 mutations, we analysed two Ccdc50 presumed loss-of-function mouse mutants which showed normal hearing thresholds up to 6 months old, thus indicating that haploinsufficiency is unlikely to be the pathogenic mechanism. We then carried out in vitro studies on a set of artificial mutants and on the p.(Asp276Glufs*40) and p.(Phe292Hisfs*37) human mutations, and determined that only the mutants containing the six amino acid sequence CLENGL as part of their aberrant protein tail showed an abnormal distribution consisting of perinuclear aggregates of the CCDC50-encoded protein Ymer. Therefore, we conclude that the CLENGL sequence is necessary to form the aggregates. Taken together the in vivo and in vitro results obtained in this study suggest that the two Spanish mutations in CCDC50 exert their effect through a dominant-negative or gain of function mechanism rather than by haploinsufficiency.

Mapping of the Cladosporium fulvum resistance gene Cf-16, a major gene involved in leaf mold disease in tomato.

Tomato (Solanum lycopersicum) is widely cultivated and consumed worldwide. Tomato leaf mold, caused by Cladosporium fulvum, is one of the most devastating diseases in tomato production. At present, some tomato leaf mold resistance (Cf series) genes used in production gradually lose resistance due to the continuous and rapid differentiation of C. fulvum physiological races. The Cf-16 gene derived from the "Ontario7816" tomato cultivar has shown effective resistance in field trials for many years, but few studies have reported on the mapping of the Cf-16 gene, which has not been cloned, limiting its utilization in tomato breeding. Here, we mapped Cf-16 using a novel comprehensive strategy including bulk segregation analysis (BSA), genome resequencing and SSR molecular markers. A genetic analysis revealed that Cf-16 resistance in "Ontario7816" is controlled by one major dominant locus. The Cf-16 gene was mapped in a region of 2.6cM at chromosome 6 between two markers, namely, TGS447 and TES312, by using an F2 population from a cross between the resistant cultivar "Ontario7816" and susceptible line "Moneymaker." Two nucleotide-binding-site-leucine-rich repeat (NBS-LRR) resistance genes, namely, XM_004240667.3 and XM_010323727.1, were identified in this interval. They are strong candidates for the Cf-16 gene. The mapping of Cf-16 may speed up its utilization for breeding resistant tomato varieties and represents an important step forward in our understanding of the mechanism underlying resistance to tomato leaf mold.

Fine genetic mapping of the Mottled Rind Color (Morc) locus reveals a 4895-bp presence-absence variation contributing to the mottled or unmottled fruit rind color in cucumber

Rind color and pattern is the crucial fruit trait that preferentially affects the commercial consumption of cucumber (Cucumis sativus L.). Knowing the genetic architecture of fruit rind color and pattern is essential for improving cucumber external qualities. However, the genetic basis of cucumber fruit rind patterns is still unclear, especially for the phenotypic variation of mottled or unmottled (uniform) fruit rind color. To explore the genetic architecture of mottled fruit rind color in cucumber, we constructed F2 segregating populations using two cucumber inbred lines WI7632 and XNS16–1 showing green mottled rind color and white uniform rind color, respectively. Inheritance analysis revealed that the mottled rind color in WI7632 is genetically controlled by a dominant locus Morc (Mottled rind color). Chlorophyll content determination and chloroplast observation show that the mottled fruit rind color in WI7632 might be due to the decrease of chlorophyll synthesis caused by abnormal chloroplast development at particular fruit rind areas. Fine genetic mapping delimited the Morc locus into a 29.5-kb physical region on chromosome 5, which included only one candidate gene CsaV3_5G028870 encoding a C2H2-type zinc finger transcription factor. Sequence alignment showed that CsaV3_5G028870 and its flanking region (4895-bp in size) were missed in unmottled XNS16–1. Transcriptome profiling revealed that Morc might regulate the biosynthesis balance of heme and chlorophyll. Furthermore, the pleiotropic effects and diverse functions of Morc locus on determining multiple cucumber fruit's external qualities were discussed.

Effects of the quantitative trait locus qPss3 on inhibition of photoperiod sensitivity and resistance to stalk rot disease in maize.

We identified a quantitative trait locus, qPss3, and fine-mapped the causal locus to a 120-kb interval in maize. This locus inhibits the photoperiod sensitivity caused by ZmCCT9 and ZmCCT10, resulting in earlier flowering by 2 ~ 4days without reduction in stalk-rot resistance in certain genotypes. Photoperiod sensitivity is a key factor affecting the adaptation of maize (Zea mays L.) to high-latitude growing areas. Although many genes associated with flowering time have been identified in maize, no gene that inhibits photoperiod sensitivity has been reported. In our previous study, we detected large differences in photoperiod sensitivity among maize inbred lines with the same photoperiod-sensitive allele at the ZmCCT10 locus. Here, we used two segregating populations with the same genetic backgrounds but different ZmCCT10 alleles to perform quantitative trait locus (QTL) analysis. We identified a unique QTL, qPss3, on chromosome 3 in the population carrying the sensitive ZmCCT10 allele. After sequential fine-mapping, we eventually delimited qPss3 to an interval of ~ 120kb. qPss3 behaved as a dominant locus and caused earlier flowering by 2-4days via inhibiting ZmCCT10-induced photoperiod sensitivity under long-day conditions. qPss3 also inhibited the photoperiod sensitivity induced by another flowering-related gene, ZmCCT9. For application in agriculture, an F1 hybrid heterozygous at both qPss3 and ZmCCT10 loci constitutes an optimal allele combination, showing high resistance to stalk rot without a significant delay in flowering time. Moreover, qPss3 is of great value in regulating the flowering time of tropical maize grown at high-latitude regions.

Map-based cloning of the APRR2 gene controlling green stigma in bitter gourd (Momordica charantia).

Bitter gourd is an economically important vegetable and medicinal crop distinguished by its bitter fruits. Its stigma color is widely used to assess the distinctiveness, uniformity, and stability of bitter gourd varieties. However, limited researches have been dedicated to genetic basis of its stigma color. In this study, we employed bulked segregant analysis (BSA) sequencing to identify a single dominant locus McSTC1 located on pseudochromosome 6 through genetic mapping of an F2 population (n =241) derived from the cross between green and yellow stigma parental lines. An F2-derived F3 segregation population (n = 847) was further adopted for fine mapping, which delimited the McSTC1 locus to a 13.87 kb region containing one predicted gene McAPRR2 (Mc06g1638), a homolog of the Arabidopsis two-component response regulator-like gene AtAPRR2. Sequence alignment analysis of McAPRR2 revealed that a 15 bp insertion at exon 9 results in a truncated GLK domain of its encoded protein, which existed in 19 bitter gourd varieties with yellow stigma. A genome-wide synteny search of the bitter gourd McAPRR2 genes in Cucurbitaceae family revealed its close relationship with other cucurbits APRR2 genes that are corresponding to white or light green fruit skin. Our findings provide insights into the molecular marker-assisted breeding of bitter gourd stigma color and the mechanism of gene regulation for stigma color.