Maternal Effects on Seed and Seedling Phenotypes in Reciprocal F 1 Hybrids of the Common Bean (Phaseolus vulgaris L.)

Factors Influencing the Emergence of Heterogeneous Populations of Common Bean (Phaseolus vulgaris L.) and Their Potential for Intercropping

The common bean is an important legume valued for its protein-rich seeds and its ability to fix nitrogen, making it a key element of crop rotation. In conventional agriculture, the emphasis is on uniformity and genetic purity to optimize crop performance and maximize yields. This is due to both the legal obligations to register varieties and the challenges of implementing breeding programs to create genetically diverse varieties. This paper focuses on the factors that influence the occurrence of heterogeneous common bean populations. The main factors contributing to this diversity have been described, including local adaptations, variable weather conditions, different pollinator species, and intricate interactions between genes controlling seed coat colour. We also discuss the benefits of intercropping common beans for organic farming systems, highlighting the improvement in resistance to diseases, and adverse environmental conditions. This paper contributes to a better understanding of common bean seed heterogeneity and the legal obligation to use heterogeneous populations.

The role of intraspecific crop-weed hybridization in the evolution of weediness and invasiveness: Cultivated and weedy radish (Raphanus sativus) as a case study

PREMISE

The phenotype of hybrids between a crop and its wild or weed counterpart is usually intermediate and maladapted compared to that of their parents; however, hybridization has sometimes been associated with increased fitness, potentially leading to enhanced weediness and invasiveness. Since the ecological context and maternal genetic effects may affect hybrid fitness, they could influence the evolutionary outcomes of hybridization. Here, we evaluated the performance of first-generation crop-weed hybrids of Raphanus sativus and their parents in two contrasting ecological conditions.

METHODS

Using experimental hybridization and outdoor common garden experiments, we assessed differences in time to flowering, survival to maturity, plant biomass, and reproductive components between bidirectional crop-weed hybrids and their parents in agrestal (wheat cultivation, fertilization, weeding) and ruderal (human-disturbed, uncultivated area) conditions over 2 years.

RESULTS

Crop, weeds, and bidirectional hybrids overlapped at least partially during the flowering period, indicating a high probability of gene flow. Hybrids survived to maturity at rates at least as successful as their parents and had higher plant biomass and fecundity, which resulted in higher fitness compared to their parents in both environments, without any differences associated with the direction of the hybridization.

CONCLUSIONS

Intraspecific crop-weed hybridization, regardless of the cross direction, has the potential to promote weediness in weedy R. sativus in agrestal and ruderal environments, increasing the chances for introgression of crop alleles into weed populations. This is the first report of intraspecific crop-weed hybridization in R. sativus.

Combining ability analysis of yield and biomass allocation related traits in newly developed wheat populations

Increasing biomass allocation to the root system may increase soil-organic carbon stocks and confer drought adaptation in water-limited environments. Understanding the genetic bases and inheritance of biomass allocation is fundamental for drought tolerance breeding and soil health. The objective of this study was to determine the general and specific combining ability, maternal effects and the mode of gene action controlling the major yield and biomass allocation related traits in wheat to identify good combiners for breeding and enhanced carbon sequestration. Ten selected wheat genotypes were crossed in a full diallel mating design, and 90 F₂ families were generated and evaluated in the field and greenhouse under drought-stressed and non-stressed conditions. Significant differences were recorded among the tested families revealing substantial variation for plant height (PH), kernels per spike (KPS), root biomass (RB), shoot biomass (SB), total plant biomass (PB) and grain yield (GY). Additive gene effects conditioned PH, SB, PB and GY under drought, suggesting the polygenic inheritance for drought tolerance. Strong maternal and reciprocal genetic effects were recorded for RB across the testing sites under drought-stressed conditions. Line BW162 had high yield and biomass production and can be used to transfer favourable genes to its progeny. The parental line LM75 maintained the general combining ability (GCA) effects in a positive and desirable direction for SB, PB and GY. Early generation selection using PH, SB, PB and GY will improve drought tolerance by exploiting additive gene action under drought conditions. Higher RB production may be maintained by a positive selection of male and female parents to capture the significant maternal and reciprocal effects found in this study.

Influence of Light of Different Spectral Compositions on Growth Parameters, Photosynthetic Pigment Contents and Gene Expression in Scots Pine Plantlets

The photoreceptors of red light (phytochromes) and blue light (cryptochromes) impact plant growth and metabolism. However, their action has been barely studied, especially in coniferous plants. Therefore, the influence of blue (maximum 450 nm), red (maximum 660 nm), white light (maxima 450 nm + 575 nm), far-red light (maximum 730 nm), white fluorescent light and dark on seed germination, growth, chlorophyll and carotenoid contents, as well as the transcript levels of genes involved in reception, photosynthesis, light and hormonal signaling of Scots pine plantlets, was investigated. The highest values of dry weight, root length and photosynthetic pigment contents were characteristic of 9-day-old plantlets grown under red light, whereas in the dark plantlet length, seed vigor, seed germination, dry weight and pigment contents were decreased. Under blue and white lights, the main studied morphological parameters were decreased or close to red light. The cotyledons were undeveloped under dark conditions, likely due to the reduced content of photosynthetic pigments, which agrees with the low transcript levels of genes encoding protochlorophyllide oxidoreductase (PORA) and phytoene synthase (PSY). The transcript levels of a number of genes involved in phytohormone biosynthesis and signaling, such as GA3ox, RRa, KAO and JazA, were enhanced under red light, unlike under dark conditions. We suggest that the observed phenomena of red light are the most important for the germination of the plantlets and may be based on earlier and enhanced expression of auxin, cytokinin, gibberellin and jasmonate signaling genes activated by corresponding photoreceptors. The obtained results may help to improve reforestation technology; however, this problem needs further study.

Unintended Consequences of Plant Domestication

Human selection on wild populations mostly favored a common set of plant traits during domestication. This process of direct selection also altered other independent traits that were not directly perceived or desired during crop domestication and improvement. A deeper knowledge of the inadvertent and undesirable phenotypic effects and their underlying genetic causes can help design strategies to mitigate their effects and improve genetic gain in crop plants. We review different factors explaining the negative consequences of plant domestication at the phenotypic and genomic levels. We further describe the genetic causes of undesirable effects that originate from the selection of favorable alleles during plant domestication. In addition, we propose strategies that could be useful in attenuating such effects for crop improvement. With novel -omics and genome-editing tools, it is relatively approachable to understand and manipulate the genetic and biochemical mechanisms responsible for the undesirable phenotypes in domesticated plants.

Comparative transcriptomic reveals the molecular mechanism of maize hybrid Zhengdan538 in response to water deficit

Heterosis, known as one of the most successful strategies for increasing grain yield and abiotic/biotic stress tolerance, has been widely exploited in maize breeding. However, the underlying molecular processes are still to be elucidated. The maize hybrid "Zhengdan538" shows high tolerance to drought stress. The transcriptomes of the seedling leaves of its parents, "ZhengA88" and "ZhengT22" and their reciprocal F₁ hybrid under well-watered and water deficit conditions, were analyzed by RNA sequencing (RNA-Seq). Transcriptome profiling of the reciprocal hybrid revealed 2994-4692 differentially expressed genes (DEGs) under well-watered and water-deficit conditions, which were identified by comparing with their parents. The reciprocal hybrid was more closely related to the parental line "ZhengT22" than to the parental line "ZhengA88" in terms of gene expression patterns under water-deficit condition. Furthermore, genes showed expression level dominance (ELD), especially the high-parental ELD (Class 3 and 5), accounted for the largest proportion of DEGs between the reciprocal F₁ hybrid and their parental lines under water deficit. These ELD genes mainly participated in photosynthesis, energy biosynthesis, and metabolism processes. The results indicated that ELD genes played important roles in hybrid tolerance to water deficit. Moreover, a set of important drought-responsive transcription factors were found to be encoded by the identified ELD genes and are thought to function in improving drought tolerance in maize hybrid plants. Our results provide a better understanding of the molecular mechanism of drought tolerance in hybrid maize.

Seedling and field assessment of wheat (Triticum aestivum L.) dwarfing genes and their influence on root traits in multiple genetic backgrounds

Deployment of the Rht-B1b and Rht-D1b dwarfing genes helped facilitate the Green Revolution to increase wheat yields globally. Much is known of the influence of these genes on plant height and agronomic performance, but not of their effects on root architecture. We assessed 29 near-isogenic lines (NILs) representing 11 Green Revolution and alternative dwarfing genes across multiple genetic backgrounds for root architecture characteristics in controlled and field environments. Genetic background did not influence plant height, but had a small and significant (P<0.05) effect on root architecture. All dwarfing gene NILs were significantly (P<0.01) shorter compared with tall controls. The Green Revolution Rht-B1b and Rht-D1b sometimes had longer seedling roots but were not different from their respective tall controls for root depth in the field. The Rht8, Rht12, and Rht18 dwarfing gene NILs produced long seminal roots in seedling pouches, and a greater maximum rooting depth (MRD) and root penetration rate (RPR) in the field. Genotypic increases in MRD and RPR were strongly correlated with increased harvest index and grain yield, particularly in dry environments. Careful root phenotyping highlights the potential of novel dwarfing genes for wheat genetic improvement under water-limited conditions.

Role of cytokinins in seed development in pulses and oilseed crops: Current status and future perspective

Cytokinins constitutes a vital group of plant hormones regulating several developmental processes, including growth and cell division, and have a strong influence on grain yield. Chemically, they are the derivatives of adenine and are the most complex and diverse group of hormones affecting plant physiology. In this review, we have provided a molecular understanding of the role of cytokinins in developing seeds, with special emphasis on pulses and oilseed crops. The importance of cytokinin-responsive genes including cytokinin oxidases and dehydrogenases (CKX), isopentenyl transferase (IPT), and cytokinin-mediated genetic regulation of seed size are described in detail. In addition, cytokinin expression in germinating seeds, its biosynthesis, source-sink dynamics, cytokinin signaling, and spatial expression of cytokinin family genes in oilseeds and pulses have been discussed in context to its impact on increasing economy yields. Recently, it has been shown that manipulation of the cytokinin-responsive genes by mutation, RNA interference, or genome editing has a significant effect on seed number and/or weight in several crops. Nevertheless, the usage of cytokinins in improving crop quality and yield remains significantly underutilized. This is primarily due to the multigene control of cytokinin expression. The information summarized in this review will help the researchers in innovating newer and more efficient ways of manipulating cytokinin expression including CKX genes with the aim to improve crop production, specifically of pulses and oilseed crops.

Genotypic variation and covariation in wheat seedling seminal root architecture and grain yield under field conditions

Greater embryo size in a large and carefully phenotyped mapping population was genetically associated with a greater number of longer seminal roots to increase grain yield in droughted field environments. Breeding modification of root architecture is challenging in field environments owing to genetic and phenotypic complexity, and poor repeatability with root sampling. Seeds from a large mapping population varying in embryo size were harvested from a common glasshouse and standardised to a common size before assessing in rolled germination paper at 12 and 20 °C for seedling growth. Differences in genotype means were large and heritabilities high (h² = 0.55-0.93) indicating strong and repeatable genotypic differences for most root traits. Seminal roots 1 to 3 were produced on all seedlings, whereas growth of seminal roots 4, 5 and 6 was associated with differences in embryo size. Increases in seminal root number from 4 to 6 per plant were strongly, genetically correlated with increases in total seminal length (r_g = 0.84, < 0.01). Multivariate analysis confirmed initiation and growth of seminal roots 1, 2 and 3, and of roots 4, 5 and 6 behaved as genetically independent (r_Pg = 0.15 ns) cohorts. Tails representing extremes in seedling root length and number were associated with significant differences in grain yield of up to 35% in droughted field environments but were not different in irrigated environments. Increases in grain yield were linked to greater lengths of seminal roots 4, 5 and 6 and were largely independent of plant height or development. This is the first report on the genetic relationship of seedling root architecture and embryo size, and potential in selection of seminal root size for accessing deep-soil moisture in droughted environments.

Farmers' Participatory Plant Selection of Lablab (Lablab purpureus (L.) Sweet) in Tanzania

Farmer-participatory breeding approach is an important component in the crop improvement of lablab (Lablab purpureus (L.) Sweet). The study was carried out to obtain the knowledge, practices and preferences of lablab through 31 lablab growing-farmers from Arusha, Kondoa, Karatu, Same and Babati districts of Tanzania toward initiating a lablab breeding program. Semi-structured questionnaires were administered and focused group discussions were held to collect data on the socio-demographic factors, production practices, constraints and farmer's preferred traits of lablab. Selection of preferred traits and accessions was also done by the farmers in the field. Results showed that the chief constraints of lablab production are pests and diseases, poor marketability, low seed quality, inadequate rainfall, expensive agrochemicals, low yield, and poor storage facilities. The major pests are pod borer (field) and bruchids (storage). Preferred traits for lablab improvement include the development of insect pests and disease-resistant varieties, early maturing, high yield, black colored seed for market, short cooking time, and dense foliage. Genotypes EK2, D360, HA4, and D96 with preferred traits were identified by farmers, which forms critical decisions in crop improvement. This study describes the current view of lablab production and generates the understanding of farmers' perceptions and preferences vital for breeding priorities and programs to increase its production, utilization and consumption.

Parent-of-Origin Effects on Seed Size Modify Heterosis Responses in Arabidopsis thaliana

Parent-of-origin effects arise when a phenotype depends on whether it is inherited maternally or paternally. Parent-of-origin effects can exert a strong influence on F1 seed size in flowering plants, an important agronomic and life-history trait that can contribute to biomass heterosis. Here we investigate the natural variation in the relative contributions of the maternal and paternal genomes to F1 seed size across 71 reciprocal pairs of F1 hybrid diploids and the parental effect on F1 seed size heterosis. We demonstrate that the paternally derived genome influences F1 seed size more significantly than previously appreciated. We further demonstrate (by disruption of parental genome dosage balance in F1 triploid seeds) that hybridity acts as an enhancer of genome dosage effects on F1 seed size, beyond that observed from hybridity or genome dosage effects on their own. Our findings indicate that interactions between genetic hybridity and parental genome dosage can enhance heterosis effects in plants, opening new avenues for boosting heterosis breeding in crop plants.

Seed morphological traits as a tool to quantify variation maintained in ex situ collections: a case study in Pinus torreyana

Understanding the within- and among-population distribution of trait variation within seed collections may provide a means to approximate standing genetic variation and inform plant conservation. This study aimed to estimate population- and family-level seed trait variability for existing seed collections of Torrey pine (Pinus torreyana), and to use these data to guide sampling of future collections. We quantified variation in 14 seed morphological traits and seedling emergence within and among Torrey pine populations. Using a simulation-based approach, we used estimates of within-population variance to assess the number of maternal families required to capture 95 % of trait variation within each existing seed collection. Substantial structure was observed both within and among Torrey pine populations, with island and mainland seeds varying in seed size and seed coat thickness. Despite morphological differences, seedling emergence was similar across populations. Simulations revealed that 83 % and 71 % of all maternal families within island and mainland seed collections respectively needed to be resampled to capture 95 % of seed trait variation within existing collections. From a conservation perspective, our results indicate that to optimize genetic diversity captured in Torrey pine seed collections, maximizing the number of maternal families sampled within each population will be necessary.

Effects of Maternal Environment on Seed Germination and Seedling Vigor of Petunia × hybrida under Different Abiotic Stresses

Seed germination and seedling vigor can be affected by environmental cues experienced by the mother plant. However, information about how the maternal environment affects seed quality is scarce in ornamental plants. This study aimed to investigate the effects of two different maternal environments on the seed germination and seedling vigor of Petunia × hybrida under a variety of abiotic stresses. Petunia mother plants were grown in either a greenhouse during the summer months or an indoor controlled-temperature-and-light environment. Collected seeds were subjected to external stressors, including polyethylene glycol (PEG), sodium chloride (NaCl), high temperature, and abscisic acid (ABA), to determine seed germination percentage and seedling vigor. Results indicated that seeds harvested from the mother plants grown in a controlled environment germinated better than seeds harvested from the mother plants grown in the greenhouse when suboptimal germination conditions were applied. Additionally, the seedlings from the controlled maternal environment performed better in both ABA and salinity stress tests than the greenhouse seedlings. Interestingly, the greenhouse seedlings displayed less reactive oxygen species (ROS) damage and lower electrolyte leakage than the controlled environment seedlings under dehydration stress. The difference in germination and seedling vigor of seeds from the two different maternal environments might be due to the epigenetic memory inherited from the mother plants. This study highlighted the strong impact of the maternal environment on seed germination and seedling vigor in Petunia and may assist in high-quality seed production in ornamental plants.

Maternal control of early life history traits affects overwinter survival and seedling phenotypes in sunflower (Helianthus annuus L.)

When cultivated and wild plants hybridize, hybrids often show intermediate phenotypic traits relative to their parents, which makes them unfit in natural environments. However, maternal genetic effects may affect the outcome of hybridization by controlling expression of the earliest life history traits. Here, using wild, cultivated and reciprocal crop-wild sunflower (Helianthus annuus L.) hybrids, we evaluated the maternal effects on emergence timing and seedling establishment in the field and on seedling traits under controlled conditions. In the field, we evaluated reciprocal crop-wild hybrids between two wild populations with contrasting dormancy (the high dormant BAR and the low dormant DIA) and one cultivar (CROP) with low dormancy. Under controlled conditions, we evaluated reciprocal crop-wild hybrids between two wild populations (BAR and RCU) and one CROP under three contrasting temperature treatments. In the field, BAR overwintered as dormant seeds whereas DIA and CROP showed high autumn emergence (~50% of planted seeds), resulting in differential overwinter survival and seedling establishment in the spring. Reciprocal crop-wild hybrids resembled their female parents in emergence timing and success of seedling establishment. Under controlled conditions, we observed large maternal effects on most seedling traits across temperatures. Cotyledon size explained most of the variation in seedling traits, suggesting that the maternal effects on seed size have cascading effects on seedling traits. Maternal effects on early life history traits affect early plant survival and phenotypic variation of crop-wild hybrids, thus, they should be addressed in hybridization studies, especially those involving highly divergent parents, such as cultivated species and their wild ancestors.

Developmental Pleiotropy Shaped the Roots of the Domesticated Common Bean (Phaseolus vulgaris)

Roots have been omitted from previous domestication analyses owing mostly to their subterranean nature. We hypothesized that domestication-associated changes in common bean (Phaseolus vulgaris) roots were due to direct selection for some aboveground traits that also affect roots, and to indirect selection of root traits that improved aboveground plant performance. To test this hypothesis, we compared the root traits of wild and domesticated accessions and performed a multistep quantitative trait locus (QTL) analysis of an intra-Andean recombinant inbred family derived from a landrace and a wild accession. Multivariate analysis of root traits distinguished wild from domesticated accessions and showed that seed weight affects many root traits of young seedlings. Sequential and methodical scanning of the genome confirmed the significant effect of seed weight on root traits and identified QTLs that control seed weight, root architecture, shoot and root traits, and shoot traits alone. The root domestication syndrome in the common bean was associated with genes that were directly selected to increase seed weight but had a significant effect on early root growth through a developmental pleiotropic effect. The syndrome was also associated with genes that control root system architecture and that were apparently the product of indirect selection.

Maternal control of seed weight in rapeseed (Brassica napus L.): the causal link between the size of pod (mother, source) and seed (offspring, sink)

Seed size/weight is one of the key traits related to plant domestication and crop improvement. In rapeseed (Brassica napus L.) germplasm, seed weight shows extensive variation, but its regulatory mechanism is poorly understood. To identify the key mechanism of seed weight regulation, a systematic comparative study was performed. Genetic, morphological and cytological evidence showed that seed weight was controlled by maternal genotype, through the regulation of seed size mainly via cell number. The physiological evidence indicated that differences in the pod length might result in differences in pod wall photosynthetic area, carbohydrates and the final seed weight. We also identified two pleiotropic major quantitative trait loci that acted indirectly on seed weight via their effects on pod length. RNA-seq results showed that genes related to pod development and hormones were significantly differentially expressed in the pod wall; genes related to development, cell division, nutrient reservoir and ribosomal proteins were all up-regulated in the seeds of the large-seed pool. Finally, we proposed a potential seed weight regulatory mechanism that is specific to rapeseed and novel in plants. The results demonstrate a causal link between the size of the pod (mother, source) and the seed (offspring, sink) in rapeseed, which provides novel insight into the maternal control of seed weight and will open a new research field in plants.

Heterosis-related genes under different planting densities in maize

Heterosis and increasing planting density have contributed to improving maize grain yield (GY) for several decades. As planting densities increase, the GY per plot also increases, whereas the contribution of heterosis to GY decreases. There are trade-offs between heterosis and planting density, and the transcriptional characterization of heterosis may explain the mechanism involved. In this study, 48 transcriptome libraries were sequenced from four inbred Chinese maize lines and their F1 hybrids. They were planted at densities of 45000 and 67500 plants ha-1. Maternal-effect differentially expressed genes (DEGs) played important roles in processes related to photosynthesis and carbohydrate biosynthesis and metabolism. Paternal-effect DEGs participated in abiotic/biotic stress response and plant hormone production under high planting density. Weighted gene co-expression network analysis revealed that high planting density induced heterosis-related genes regulating abiotic/biotic stress response, plant hormone biosynthesis, and ubiquitin-mediated proteolysis, but repressed other genes regulating energy formation. Under high planting density, maternal genes were mainly enriched in the photosynthesis reaction center, while paternal genes were mostly concentrated in the peripheral antenna system. Four important genes were identified in maize heterosis and high planting density, all with functions in photosynthesis, starch biosynthesis, auxin metabolism, gene silencing, and RNAi.

Differential transcriptome patterns associated with early seedling development in a wild and a domesticated common bean (Phaseolus vulgaris L.) accession

Genes that control "Domestication Syndrome" traits were direct targets of selection, like those controlling increased seed size in the common bean. However, selection for this trait brought about unintentional selection on genes controlling seedling growth. We hypothesized that wild and domesticated plants have different early seedling growth patterns as an indirect consequence of selection for a larger seed size during domestication, and those differences resulted from changes in gene expression patterns of the wild ancestor. Large seeds pose a challenge to reserve remobilization during early heterotrophic growth, particularly during a transition towards more fertile alluvial soils. To address our hypothesis, we characterized the patterns of gene expression of cotyledon, root, and leaf tissues of 7-day old seedlings of a wild and a landrace accession of the common bean. Differential expression analyses detected genes with contrasting patterns of expression between the two genotypes in all three tissues. Some of the differentially expressed genes with contrasting genotypic patterns are known to have domestication-related signatures of selection. Among these genes were some transcription factors associated with key roles in development. These genes may represent targets of indirect selection and ultimately explain the growth phenotypic differences between wild and domesticated seedlings.