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Key messageTy-6 is a major resistance gene on chromosome 10 of tomato that provides resistance against monopartite and bipartite begomoviruses and complements resistance conferred by the known Ty-3 and ty-5 genes.Resistance to monopartite and bipartite begomoviruses is an important breeding objective for cultivated tomato. Several begomovirus resistance genes have been introgressed from related Solanum species and are available for breeding purposes. In the present study, we mapped an additional locus, Ty-6, to chromosome 10 of tomato. Ty-6 is effective against both monopartite Tomato yellow leaf curl virus (TYLCV) and bipartite Tomato mottle virus (ToMoV). Gene action is incomplete dominance, with an intermediate resistance response when Ty-6 is heterozygous. Analysis of populations segregating for Ty-6 along with Ty-3 or ty-5 indicates that the highest level of resistance against TYLCV is attained when Ty-6 is combined with an additional resistance allele. Our results also demonstrate that ty-5 is ineffective against ToMoV. Although multiple SNPs linked to Ty-6 were identified and can be used for breeding purposes, none of these were consistently polymorphic between Ty-6 and ty-6 breeding lines. Further research is underway to generate resequencing data for several Ty-6 inbred lines for the discovery of additional sequence polymorphisms that can be used for fine mapping and characterizing the Ty-6 locus.

Summary The exploitation of heterosis to integrate parental advantages is one of the fastest and most efficient ways of rice breeding. The genomic architecture of heterosis suggests that the grain yield is strongly correlated with the accumulation of numerous rare superior alleles with positive dominance. However, the improvements in yield of hybrid rice have shown a slowdown or even plateaued due to the limited availability of complementary superior alleles. In this study, we achieved a considerable increase in grain yield of restorer lines by inducing an alternative splicing event in a heterosis gene OsMADS1 through CRISPR‐Cas9, which accounted for approximately 34.1%–47.5% of yield advantage over their corresponding inbred rice cultivars. To achieve a higher yield in hybrid rice, we crossed the gene‐edited restorer parents harbouring OsMADS1GW3p6 with the sterile lines to develop new rice hybrids. In two‐line hybrid rice Guang‐liang‐you 676 (GLY676), the yield of modified hybrids carrying the homozygous heterosis gene OsMADS1GW3p6 significantly exceeded that of the original hybrids with heterozygous OsMADS1. Similarly, the gene‐modified F1 hybrids with heterozygous OsMADS1GW3p6 increased grain yield by over 3.4% compared to the three‐line hybrid rice Quan‐you‐si‐miao (QYSM) with the homozygous genotype of OsMADS1. Our study highlighted the great potential in increasing the grain yield of hybrid rice by pyramiding a single heterosis gene via CRISPR‐Cas9. Furthermore, these results demonstrated that the incomplete dominance of heterosis genes played a major role in yield‐related heterosis and provided a promising strategy for breeding higher‐yielding rice varieties above what is currently achievable.

BackgroundGrain chalkiness is one of important factors affected rice grain quality. It is known that chalkiness is affected by the high temperature during the seed filling period. Although a larger of QTLs for chalkiness were reported across all 12 chromosomes, only a few of the QTLs were fine mapped or cloned up to now. Here, we fine map two QTLs for chalkiness in two single-segment substitution lines (SSSLs), 11–09 with substitution segment from O. sativa and HP67–11 with substitution segment from O. glaberrima.ResultsThe grain chalkiness of SSSLs 11–09 and HP67–11 was significantly lower than that in the recipient Huajingxian 74 (HJX74) in consecutive 8 cropping seasons. The regression correlation analysis showed that percentage of chalky grain (PCG) and percentage of chalky area (PCA) were significantly and positively correlated with percentage of grain chalkiness (PGC). Two QTLs for grain chalkiness were located on two chromosomes by substitution mapping. qPGC9 was mapped on chromosome 9 with an estimated interval of 345.6 kb. qPGC11 was located on chromosome 11 and delimited to a 432.1 kb interval in the O. sativa genome and a 332.9 kb interval in the O. glaberrima genome. qPGC11 is a QTL for grain chalkiness from O. glaberrima and was mapped in a new region of chromosome 11. The effect of two QTLs was incomplete dominance. The additive effects of two QTLs on chalkiness in second cropping season (SCS) were significantly greater than that in first cropping season (FCS).ConclusionsqPGC11 is a new QTL for grain chalkiness. The two QTLs were fine mapped. The donor alleles of qPGC9 and qPGC11 were sensitive to the high temperature of FCS.

Castor bean ( Ricinus communis L.), is a commercially significant oilseed crop, valued for its high oil content and diverse applications. The Castor whitefly ( Trialeurodes ricini Misra) is a multivoltine tropical pest that causes substantial yield losses, particularly during rabi and summer season. Morphological markers in castor are abundant, with bloom type being associated with whitefly resistance. This study investigated the relationship between bloom type and whitefly resistance by screening 29 genotypes with varying bloom types. The results demonstrated that double and triple bloom types are highly susceptible to whiteflies, whereas zero and single bloom types exhibited high resistance. The F 1 generations from crosses among different bloom types displayed susceptibility to whiteflies, except for the cross between zero and single bloom, which exhibited a single bloom phenotype. In the cross between bloom and no bloom (DPC 9 × TMV 5) monogenic dominant nature for bloom was observed. Genetic characterization of whitefly resistance in this cross indicated a monogenic recessive nature for whitefly resistance. It is suggested that bloom and whitefly resistance may be tightly linked in a repulsion phase or may involve the pleiotropic effect of a single gene. These findings were further corroborated by the cross between M 619-1 × SKI 215. Additionally, the study demonstrated monogenic incomplete dominance of triple bloom over zero bloom and monogenic complete dominance of triple bloom over double bloom.

Key messageCpDll, encoding an HD-Zip I transcription factor, positively regulates formation of deeply lobed leaf shape in zucchini, Cucurbita pepo, which is associated with sequence variation in its promoter region.Leaf shape is an important horticultural trait in zucchini (Cucurbita pepo L.). Deeply lobed leaves have potential advantages for high-density planting and hybrid production. However, little is known about the molecular basis of deeply lobed leaf formation in this important vegetable crop. Here, we conducted QTL analysis and fine mapping of the deeply lobed leaf (CpDll) locus using recombinant inbred lines and large F2 populations developed from crosses between the deeply lobed leaf HM-S2, and entire leaf Jin-GL parental lines. We show that CpDll exhibited incomplete dominance for the deeply lobed leaf shape in HM-S2. Map-based cloning provided evidence that CpCll encodes a type I homeodomain (HD)- and Leu zipper (Zip) element-containing transcription factor. Sequence analysis between HM-S2 and Jin-GL revealed no sequence variations in the coding sequences, whereas a number of variations were identified in the promoter region between them. DUAL-LUC assays revealed significantly stronger promoter activity in HM-S2 than that in Jin-GL. There was also significantly higher expression of CpDll in the leaf base of deeply lobed leaves of HM-S2 compared with entire leaf Jin-GL. Comparative analysis of CpDll gene homologs in nine cucurbit crop species (family Cucurbitaceae) revealed conservation in both structure and function of this gene in regulation of deeply lobed leaf formation. Our work provides new insights into the molecular basis of leaf lobe formation in pumpkin/squash and other cucurbit crops. This work also facilitates marker-assisted selection for leaf shape in zucchini breeding.

Periwinkle ( Catharanthus roseus L.) is an ornamental and therapeutic herbaceous subshrub. The available literature on inheritance of flower colour in periwinkle is meager. The present investigation was conducted at the Punjab Agricultural University, Ludhiana to exploit the genetic inheritance of flower colour and to determine the number of genes involved in the inbred lines of periwinkle by crossing of an accession Vi-15-1 possessing magenta with white centre corolla and another accession Vi-29 possessing white corolla. The all F 1 plants developed from crossing, including reciprocal were shown pale purple coloured flowers. In the F 2 generation, three types of plants were generated such as magenta with white centre corolla ( O m O m ), pale purple corolla ( O m W ) and white ( WW ) corolla in the ratio of 1:2:1. The results indicate that magenta corolla shows incomplete dominance over white corolla which is possibly governed by a single pair of gene. The reciprocal cross reported the same results indicating no involvement of the cytoplasmic genes in this process. Since it is crucial to improve the landscaping traits genetically in periwinkle hence, in light of this; the present study on inheritance of corolla colour may be able to serve as future reference for the valuable genetic research.

Acidity and sweetness are important qualities for apple breeders and understanding their genetic regulation can improve the breeding process. In previous QTL studies, fruit quality assessments were performed using instrumental measurements, leading to the identification of two major QTL Ma and Ma3. Here, we use sensorial data to investigate the role of known and unknown genetic factors in the perception of acidity and sweetness in three pedigreed full-sib families. For 2 years, these families were phenotyped by a trained panel, at harvest and after 2 months of cold storage, and genotyped with a new 50 K SNP array. FlexQTLTM analyses using both an additive and an additive + dominance model resulted in the identification of Ma and Ma3 for acidity as well as sweetness, whereas the use of the additive model yielded decisive evidence for the discovery of two additional QTL on LG1 and LG6 for acidity. QTL genotypes were qualified as the inverse of each other, which indicates that individuals with the less-acidity alleles of Ma and Ma3 are perceived sweeter. Due to the genetic configuration in the families studied, resulting from a link with the Pale Green Disorder locus, no incomplete dominance effect could be detected for the Ma locus, although previously reported in the literature. For the Ma3 locus, however, an incomplete dominance effect (58%) is reported here for the first time. The Ma3 locus was also further confined to a 2–4-cM region and a predictive marker for this locus was identified.

Key messageApart from confinement of Ne1 to a 4.45 Mb genomic segment, markers closely linked to Ne2 were identified and incomplete dominance of both genes in conditioning necrosis severity was shown.Hybrid necrosis in plants is characterized by premature death of leaves or plants in F1 hybrids. Interaction of two complementary dominant genes Ne1 and Ne2 in wheat (Triticum aestivum L.) is known to cause hybrid necrosis. However, the mechanism underlying this necrosis is still elusive. To obtain markers closely-linked to these two genes, Ne1-carrying cultivar Zheng891 was crossed with Ne2-carrying cultivar Pan555. Using BC1F1 plants derived from crosses of the F1 plants with the two parental lines, Ne1 and Ne2 were mapped to a 2.2 cM interval and a 2.3 cM interval with newly developed markers, respectively. Ne1 was further delimited to a 0.19 cM interval using 2015 Ne2-carrying F2 plants. Xwgrc3146, Xwgrc3147 and Xwgrc3150, three of the four markers co-segregating with Ne1, were all Zheng891-dominant, suggesting that, compared with Pan555, Ne1 is located in a region with substantial sequence diversity. The Ne1 interval is syntenic to chromosomes 5H, 4, 9 and 2 of barley, Brachypodium distachyon, rice and sorghum, respectively, and corresponds to a 4.45 Mb Chinese Spring sequence. Variations in necrosis severity of the F2 plants differing in Ne1 and Ne2 genotypes implied that these two genes are incompletely dominant in determining the timing and severity of necrosis.

The main objective in this research was the genetic analysis of heterosis in rapeseed at the QTL level. A linkage map comprising 235 SSR and 144 AFLP markers covering 2045 cM was constructed in a doubled-haploid population from a cross between the cultivar “Express” and the resynthesized line “R53.” In field experiments at four locations in Germany 250 doubled-haploid (DH) lines and their corresponding testcrosses with Express were evaluated for grain yield and three yield components. The heterosis ranged from 30% for grain yield to 0.7% for kernel weight. QTL were mapped using three different data sets, allowing the estimation of additive and dominance effects as well as digenic epistatic interactions. In total, 33 QTL were detected, of which 10 showed significant dominance effects. For grain yield, mainly complete dominance or overdominance was observed, whereas the other traits showed mainly partial dominance. A large number of epistatic interactions were detected. It was concluded that epistasis together with all levels of dominance from partial to overdominance is responsible for the expression of heterosis in rapeseed.

Watermelon is an important horticultural crop in the Cucurbitaceae family, which exhibits a remarkable diversity of vegetative phenotypes. In this experimental study, two contrasted watermelon lines “natural mutant line (DW-2) with non-lobed leaves and the wild-type line (DG-2) with lobed leaves” were crossed to derive the biparental F2 mapping populations over two years. Genetic segregation analysis suggested that the non-lobed leaf (nll) phenotype is controlled by a single genetic locus with incomplete dominance. Bulk segregant sequencing analysis (BSA-seq) and preliminary linkage mapping with 183 F2 individuals identified the nll locus in a 0.7 Mbp region on chromosome 4, which was also verified in a genome-wide association study (GWAS) of 144 watermelon accessions with leaf variations. Fine genetic mapping with a large F2 population (n = 1069) and screened recombinants exposed the delimited candidate region of 98.23 kb with eight functionally annotated genes. The sequence analysis in this region suggested that Cla97C04G076510 is the most likely candidate gene for regulating the nll, which encodes a homeobox leucine zipper (HD-Zip) transcription factor (ClNll), a homolog of the LATE MERISTEM IDENTITY1 (LMI1) in Arabidopsis. A single nucleotide deletion in the second exon of nll was mainly responsible for the non-lobed leaf phenotype, which encoded a truncated protein. A genetic marker based on the 1-bp deletion showed co-segregation with leaf lobeness in the F2 population, exhibiting validation in the natural GWAS panel of 144 watermelon accessions. The phylogenetic associations of ClNll protein sequences with 11 homologous sequences from eight other plant species revealed an identical conserved function. Further, the expression level of the Cla97C04G076510 gene was noticed to be significantly lower in the non-lobed leaf of the DW-2 mutant. The identified results provide valuable insights for understanding the genetic regulation of leaf shape variation in watermelon and would be helpful for marker-assisted breeding aimed at the development of improved cultivars.