Inheritance of growth habit under photoperiod insensitive genetic background in dolichos bean (Lablab purpureus (L.) Sweet)

Development of high yielding cultivars with determinate growth habit in photoperiod insensitive (PIS) background is one of the major objectives of breeding grain legumes crops including dolichos bean. A thoroughly validated genetic basis is a prerequisite for breeding dolichos bean for determinate growth habit in PIS background. Based on the published reports by researchers of our laboratory and those by others, and our unpublished data, we hypothesized that the number and mode of action of genes controlling growth habit differ with degree of photoperiod sensitivity of the genetic material used to investigate the inheritance of growth habit in dolichos bean. To test this hypothesis, we compared the number and mode of action of genes controlling growth habit between segregating generations in Photoperiod sensitive (PS) and those in PIS genetic backgrounds. While indeterminate and determinate plants segregated in 15:1 ratio in F2 populations derived from crosses between determinate PIS and indeterminate PIS parents, they segregated in 9:7 ratio with indeterminacy being dominant in F2 populations derived from crosses between determinate PIS and indeterminate PS parents. These patterns of segregation (15:1 and 9:7) in favour of indeterminate and determinate plants, respectively in F2 populations were confirmed in F3 populations of PIS and PS genetic backgrounds based on good fit between observed and expected ratios (55:9 and 29:35, respectively) in favour of indeterminate and determinate plants, respectively. The patterns of segregation in F2 populations were further confirmed in F3 populations based on good fit between observed and expected ratios of 3:1 segregating and non-segregating families, and of 3:1 indeterminate and determinate non-segregating families, respectively.

Genome-Wide Analysis of the Phospholipase D Family in Five Cotton Species, and Potential Role of GhPLD2 in Fiber Development and Anther Dehiscence

Phospholipase D (PLD) and its hydrolysis product phosphatidic acid play an important role in the regulation of several cellular processes, including root growth, pollen tube elongation, and microtubule reorganization. Here, we systematically identified and analyzed the membership, characterization, and evolutionary relationship of PLDs in five species of cotton. The results of the transcriptomic analysis suggested that the evaluated PLD genes showed high expression levels in anther tissue and during the fiber initiation and elongation periods. Quantitative real-time polymerase chain reaction showed differential expression of GhPLD genes in the anthers of photoperiod sensitive male sterility mutant 5 (psm5). Previous research on multiple stable quantitative trait loci also suggests the role of PLD genes in the fiber development. Further analyses showed that GhPLD2 protein is localized to the plasma membrane. The virus-induced gene silencing of GhPLD2 in cotton seedlings repressed its expression by 40–70%, which led to a reduction in reactive oxygen species (ROS) levels, 22% anther indehiscence, and disrupted fiber initiation and elongation. Thus, we inferred that GhPLD2 may promote ROS production, which, in turn, may regulate anther dehiscence and fiber development.

DNA methylation affects photoperiodic tuberization in potato (Solanum tuberosum L.) by mediating the expression of genes related to the photoperiod and GA pathways

Overcoming short-day-dependent tuberization to adapt to long-day conditions is critical for the widespread geographical success of potato. The genetic pathways of photoperiodic tuberization are similar to those of photoperiodic flowering. DNA methylation plays an important role in photoperiodic flowering. However, little is known about how DNA methylation affects photoperiodic tuberization in potato. Here, we verified the effect of a DNA methylation inhibitor on photoperiodic tuberization and compared the DNA methylation levels and differentially methylated genes (DMGs) in the photoperiodic tuberization process between photoperiod-sensitive and photoperiod-insensitive genotypes, aiming to dissect the role of DNA methylation in the photoperiodic tuberization of potato. We found that a DNA methylation inhibitor could promote tuber initiation in strict short-day genotypes. Whole-genome DNA methylation sequencing showed that the photoperiod-sensitive and photoperiod-insensitive genotypes had distinct DNA methylation modes in which few differentially methylated genes were shared. Transcriptome analysis confirmed that the DNA methylation inhibitor regulated the expression of the key genes involved in the photoperiod and GA pathways to promote tuber initiation in the photoperiod-sensitive genotype. Comparison of the DNA methylation levels and transcriptome levels identified 52 candidate genes regulated by DNA methylation that were predicted to be involved in photoperiodic tuberization. Our findings provide a new perspective for understanding the relationship between photoperiod-dependent and GA-regulated tuberization. Uncovering the epigenomic signatures of these pathways will greatly enhance potato breeding for adaptation to a wide range of environments.

Structural And Functional Analysis of CCT Family Genes In Pigeonpea

Pigeonpea (Cajanus cajan (L) Millsp) is a short-day plant in which the flowering is highly sensitive to photoperiod. A better understanding of the genes modulating photoresponse and flowering time is critical to developing photoperiod insensitive pigeonpea cultivars for cultivation across the seasons. We identified 33 CCT family genes (CcCCT1- CcCCT33) in C. cajan and localized them on 10 chromosomes and nine genomic scaffolds. The structural analysis of CCT family genes revealed a considerable variation in length and distribution of exons and introns. Based on the type of domain(s), we classified the CCT family genes into CCT motif family (CMF) type, CONSTANS like (COL) type, Pseudo-response Regulator (PRR) type, and GATA and tifi containing CCT (GTCC) type. The CCT family genes of C. cajan exhibited an extensive orthologous relationship with the CCT family genes of other legume species. We also observed significant sharing of CCT family genes among the legume species. Glycine max exhibited the maximum sharing of CCT family genes with C. cajan. The analysis of CCT family proteins-based phylogenic relationships revealed a general congruence with the legumes' taxonomic relationships. The expression analysis of CCT family genes of pigeonpea demonstrated that CcCCT4 and CcCCT23 are the active CONSTANS (CO) in ICP20338. In contrast, only CcCCT23 is active in MAL3, explaining the differential response of ICP20338 and MAL3 to photoperiod. The chromosomes of C. cajan contain a variable number of CCT family genes. A majority of these genes are localized in the centromeric regions. The COL type CCT genes are structurally highly diverse and contain a variable number of B-box domains. The CCT family genes of different legume species exhibit all three kinds of relationships: one-to-one, many-to-one, and many-to-many types. The photoperiod insensitive cultivar ICP20338 contains CcCCT4 and CcCCT23, while the photoperiod sensitive cultivar MAL3 contains only CcCCT23 as active CONSTANS (CO), which may be the plausible reason for their differential photoperiod response.

Genetic and Transcriptomic Analysis Reveal the Molecular Basis of Photoperiod-Regulated Flowering in Xishuangbanna Cucumber (Cucumis sativus L. var. xishuangbannesis Qi et Yuan)

Xishuangbanna (XIS) cucumber (Cucumis sativus L. var. xishuangbannesis Qi et Yuan), is a botanical variety of cucumber cultivars native to southwest China that possesses excellent agronomic traits for cucumber improvement. However, breeding utilization of XIS cucumber is limited due to the current poor understanding of its photoperiod-sensitive flowering characteristics. In this study, genetic and transcriptomic analysis were conducted to reveal the molecular basis of photoperiod-regulated flowering in XIS cucumber. A major-effect QTL locus DFF1.1 was identified that controls the days to first flowering (DFF) of XIS cucumbers with a span of 1.38 Mb. Whole-genome re-sequencing data of 9 cucumber varieties with different flowering characteristics in response to photoperiod suggested that CsaNFYA1 was the candidate gene of DFF1.1, which harbored a single non-synonymous mutation in its fifth exon. Transcriptomic analysis revealed the positive roles of auxin and ethylene in accelerating flowering under short-day (SD) light-dark cycles when compared with equal-day/night treatment. Carbohydrate storage and high expression levels of related genes were important reasons explaining early flowering of XIS cucumber under SD conditions. By combining with the RNA-Seq data, the co-expression network suggested that CsaNFYA1 integrated multiple types of genes to regulate the flowering of XIS cucumber. Our findings explain the internal regulatory mechanisms of a photoperiodic flowering pathway. These findings may guide the use of photoperiod shifts to promote flowering of photoperiod-sensitive crops.

Quantitative Trait Loci and Candidate Genes Associated with Photoperiod Sensitivity in Lettuce (Lactuca spp.)

Key message A population of lettuce that segregated for photoperiod sensitivity was planted under long-day and short-day conditions. Genetic mapping revealed two distinct sets of QTLs controlling daylength-independent and photoperiod-sensitive flowering time. Abstract The molecular mechanism of flowering time regulation in lettuce is of interest to both geneticists and breeders because of the extensive impact of this trait on agricultural production. Lettuce is a facultative long-day plant which changes in flowering time in response to photoperiod. Variations exist in both flowering time and the degree of photoperiod sensitivity among accessions of wild (Lactuca serriola) and cultivated (L. sativa) lettuce. An F6 population of 236 recombinant inbred lines (RILs) was previously developed from a cross between a late-flowering, photoperiod-sensitive L. serriola accession and an early-flowering, photoperiod-insensitive L. sativa accession. This population was planted under long-day (LD) and short-day (SD) conditions in a total of four field and screenhouse trials; the developmental phenotype was scored weekly in each trial. Using genotyping-by-sequencing (GBS) data of the RILs, quantitative trait loci (QTL) mapping revealed five flowering time QTLs that together explained more than 20% of the variation in flowering time under LD conditions. Using two independent statistical models to extract the photoperiod sensitivity phenotype from the LD and SD flowering time data, we identified an additional five QTLs that together explained more than 30% of the variation in photoperiod sensitivity in the population. Orthology and sequence analysis of genes within the nine QTLs revealed potential functional equivalents in the lettuce genome to the key regulators of flowering time and photoperiodism, FD and CONSTANS, respectively, in Arabidopsis.

Establishment of Alternative Season for Cultivation of Photoperiod-Sensitive Traditional Rice Cultivars

Aims: To find out the suitable time for cultivating the photoperiod-sensitive rice cultivars during off-season. Study Design: Randomized Block Design. Place and Duration of Study: University Research Farm, Uttar Banga Krishi Viswavidyalaya, Pundibari, Cooch Behar 736165, West Bengal, India. Experiments were conducted during Boro 2017 and Kharif 2018. Methodology: Forty nine cultivars were sown in seed beds on 28th November, 2017 for cultivation of the Boro crop and sowing was done on 30th June, 2018 for cultivation of Kharif crop. Seedlings were transplanted in randomized block design with two replications. Row to row spacing was 30 cm and plant to plant spacing was 20 cm. Standard agronomic practices compatible to the humid tropic of Terai Zone were practiced. Ten random plants from each plot were selected for recording data. Observations were recorded on yield and yield attributing parameters. Results: High significant variation was observed for all the characters under study indicating the presence of high variability among the selected cultivars. Only the test weight between the two seasons had insignificant difference representing that there was no effect of seasons on this character. Time of sowing was standardized for sowing of the traditional cultivars in alternative season- Boro. The yield ranged from 0.35 t/ha to 2.68 t/ha during Boro and from 2.67 t/ha to 8.48 t/ha during Kharif. Ronga Komal (2.68 t/ha), Kauka (2.65 t/ha), Jaldhyapa (2.54 t/ha), Chakhao Angangbi (2.07 t/ha), Kaloboichi (1.87 t/ha), Kalturey (1.85 t/ha), Chakhao-Selection-2 (1.59 t/ha), Chakhao-Selection-1 (1.46 t/ha), Chakhao Sempak (1.43 t/ha) and Chakhao-Selection-3 (1.42 t/ha) performed well during Boro season. Conclusion: Ronga Komal, Kauka, Jaldhyapa, Chakhao Angangbi, Kaloboichi, Kalturey, Chakhao-Selection-2, Chakhao-Selection-1, Chakhao Sempak and Chakhao-Selection-3 performed well during Boro season. Consequently, those above varieties may be recommended for cultivation during Boro season.

Variation for Photoperiod and Temperature Sensitivity in the Global Mini Core Collection of Sorghum

Information on photoperiod and temperature sensitivity of sorghum germplasm is important to identify appropriate sources for developing cultivars with a broad adaptation. The sorghum mini core collection consisting of 242 accessions along with three control cultivars were evaluated for days to 50% flowering (DFL) and plant height in two long-day rainy and two short-day post-rainy seasons, and for grain yield and 100-seed weight in the two post-rainy seasons. Differences in DFL and cumulative growing degree days (CGDD) in the rainy and post-rainy seasons were used to classify the accessions for photoperiod and temperature sensitivity. Results revealed 18 mini core landraces as photoperiod and temperature insensitive (PTINS), 205 as photoperiod sensitive and temperature insensitive (PSTINS), and 19 as photoperiod and temperature-sensitive (PTS) sources. The 19 PTS sources and 80 PSTINS sources took less DFL in the long-day rainy seasons than in the short-day post-rainy season indicating their adaptation to the rainy season and a possible different mechanism than that trigger flowering in the short-day sorghums. In all three groups, several accessions with desirable combinations of agronomic traits were identified for use in the breeding programs to develop climate-resilient cultivars and for genomic studies to identify genes responsible for the photoperiod and temperature responses.