Pod Traits Research Articles

Identifying the Numerical Components Affecting Soybean (Glycine max) Yield Under Waterlogging at Reproductive Stages

ABSTRACTWaterlogging is a critical abiotic stress increasing in importance due to more intense, erratic rainfall associated with climate change. Waterlogging leads to significant yield losses in sensitive crops, such as soybean (Glycine max [L.] Merr.). Identifying soybean genotypes and traits associated with better waterlogging tolerance is of high interest. We assessed the response of six soybean genotypes, selected from a field screening of over 190 genotypes, to 10 days of waterlogging at the R1 (onset of flowering) and R4 (grain filling) stages. We evaluated yield and its components, as well as shoot and root dry weights (DW) at the end of the waterlogging treatments and at maturity, along with morphological traits such as plant branch number, stem diameter and plant height. By integrating all these traits, a waterlogging tolerance index (WTI) was calculated for each genotype to rank their sensitivity. The WTI showed variations among genotypes from 0.61 to 0.77, indicating genotypic variation in response to waterlogging. Greater reductions in root DW compared to shoot DW were observed immediately after waterlogging. By maturity, shoot DW of waterlogged plants was more severely reduced than root DW in all genotypes. Despite similar DW losses at R1 and R4 at physiological maturity, seed number per plant and 100‐seed weight responses differed between the treatments. Genotypes that performed well under control conditions suffered significant yield reductions of 70%–85% after waterlogging, mainly due to fewer fertile nodes and seeds per pod, with some also experiencing a notable decrease in 100‐seed weight. In contrast, other genotypes had milder responses, with less severe reductions in seed and pod traits. Identifying breeding soybean genotypes tolerant to waterlogging during reproductive stages that maintain the number of fertile nodes and pods per node without changes in seeds per pod could significantly mitigate yield losses from waterlogging.

Genome-wide association study of appearance quality traits and development of KASP makers in vegetable soybean

Vegetable soybean [(Glycine max (L.) Merr.], commonly referred to as edamame, holds significant agricultural importance in China as a legume vegetable harvested at the pod-filling stage (R6). The visual appeal of vegetable soybeans, crucial for consumer preference and marketability, depends on factors such as pod length, pod width, and pod color. This study cultivated 264 vegetable soybeans in Nanjing, Huai'an, and Nantong to assess pod traits using PlantPhenoM, a system for pod phenotypic identification and analysis. Results revealed a variability range of 8.64 to 30.00% in appearance quality traits among vegetable soybeans. Leveraging phenotypic data and employing a genome-wide association study (GWAS) we identified 525 SNPs significantly linked to appearance quality traits in different regions. In addition, candidate genes (Glyma.04G004700, Glyma.15G051600, Glyma.18G225700, Glyma.18G225900, and Glyma.18G272300) associated with target traits were identified, and KASP markers for S04_372771 (pod length), S18_51477324 (pod width), and S18_55553200 (pod color) were developed, respectively. This research offers valuable insights for breeding superior vegetable soybean varieties and lays the groundwork for exploring candidate genes and molecular markers related to appearance and quality traits in vegetable soybeans.

Characterization and Performance Evaluation of Liquid Biodegradable Mulch Films and Its Effects on Peanut Cultivation.

With the development of material science and increasing awareness of ecological environmental protection, liquid biodegradable mulch films (LBDMs) have garnered significant public interest. In this research, new LBDMs were developed using hydrophobically modified polymer materials, surfactants, and photosensitive catalysts. Characterization by scanning electron microscopy (SEM) revealed good material compatibility. LBDMs exhibited excellent wettability and degradability, effectively covering soil surfaces and enhancing soil moisture conservation, with a degradation rate of 76.09% after 80 days of burial. The field performance experiment was conducted over two consecutive years, 2021 and 2022, to assess differences in soil temperature and moisture, peanut agronomic traits, pod traits, and yield under four treatments: non-mulching (CK), LBDMs, clear polyethylene mulch films (CPEMs), and black polyethylene mulch films (BPEMs). LBDMs increased soil temperature by 0.56 °C and soil moisture by 19.25%, accelerated the seedling stage by 4-to-6 days, and improved the average emergence rate by 15.91%. Furthermore, LBDMs significantly promoted peanut growth, and it increased yield by 14.34% compared to CK. LBDMs performed comparably to the two types of PE films in maintaining soil conditions and different crop phenotype traits, including plant height, branch number, yield, and quality, and they even outperformed PE films in productivity per plant and 100-kernel weight. These findings suggest that LBDMs are a promising eco-friendly alternative to traditional PE films.

Genetic inheritance of leaf and pod traits in blackgram [Vigna mungo (L.) Hepper]

Genetic inheritance of leaf and pod traits in blackgram [Vigna mungo (L.) Hepper]

Phenotypic characterization of ethyl methanesulfonate (EMS) induced bigger pod (bp) with multiple seed mutant in lentil (Lens culinaris Medik.)

Lentils (Lens culinaris Medik.) is a protein- and nutrient-rich crop with limited genetic diversity and climate adaptability, making it ideal for mutation breeding research. Hence, in this study, we aimed to select and characterize distinct mutations in the flower and pod traits of lentil crops for enhanced yield and yield stability. In this study, healthy and viable lentil seeds were mutagenized using different concentrations of ethyl methanesulfonate (EMS) (0.10%, 0.25%, 0.50%, 0.75%, and 1.0%). The mutagenized lentil populations were cultivated up to the third generation (M3) to identify stable mutations in the flower and pod structures with increasing plant height. The notably larger 'bigger pod’ (bp) mutant, characterized by its unusually large pods containing 6–7 seeds per pod, was meticulously studied and quantified for its morphological traits in subsequent generations. Morphological observations of the tall bp mutant revealed significant mutations induced by EMS (0.10%) treatment. The quantitative trait means and confidence intervals showed that the mutant and parent cultivar L-4076 exhibited considerable variation. Seed yield (g) and yield-related components, including pods per plant, pod length (cm), and seeds per pod, were significantly higher in the mutant. Seed yield exhibited a significant positive phenotypic correlation with pod length, followed by branches per plant, seeds per pod, plant height, and pods per plant. The novel bp mutant induced in the present study produced increased number of seeds per plant and ensured optimal resource utilization, thus possibly contributing to yield improvement and stability. Further, it also aided in understanding the genetic networks that control legume flower and pod architecture and in genomics-assisted breeding for the development of superior lentil cultivars.

Genome-Wide Association Study and Identification of Candidate Genes Associated with Seed Number per Pod in Soybean.

Soybean (Glycine max [L.] Merr.) is one of the primary sources of plant protein and oil for human foods, animal feed, and industrial processing. The seed number per pod generally varies from one to four and is an important component of seed number per unit area and seed yield. We used natural variation in 264 landraces and improved cultivars or lines to identify candidate genes involved in the regulation of seed number per pod in soybean. Genome-wide association tests revealed 65 loci that are associated with seed number per pod trait. Among them, 11 could be detected in multiple environments. Candidate genes were identified for seed number per pod phenotype from the most significantly associated loci, including a gene encoding protein argonaute 4, a gene encoding histone acetyltransferase of the MYST family 1, a gene encoding chromosome segregation protein SMC-1 and a gene encoding exocyst complex component EXO84A. In addition, plant hormones were found to be involved in ovule and seed development and the regulation of seed number per pod in soybean. This study facilitates the dissection of genetic networks underlying seed number per pod in soybean, which will be useful for the genetic improvement of seed yield in soybean.

Genome-wide Association Study Identifies Candidate Loci with Major Contributions to the Genetic Control of Pod Morphological Traits in Snap Bean

Snap beans are cultivars of common bean (Phaseolus vulgaris) that are cultivated for their fleshy immature pods that exhibit a wide diversity of pod shapes and sizes. The genetic basis of the snap bean pod shape is complex and involves the interaction of multiple genes. This study used a snap bean diversity panel composed of heirloom and improved cultivars used in North America and genome-wide association studies (GWAS) to investigate the genetic basis of pod morphological characteristics, including length, width, height, width/height ratio, and coefficients of variation (CVs). The GWAS detected multiple genomic regions associated with each pod trait, with a total of 20 quantitative trait loci (QTLs) for pod length, 9 for pod width, 14 for pod height, and 10 for pod width/height ratio. Regarding the CV of each pod trait, genome-wide association analyses detected six QTL for length CVs, five for width CVs, 15 for height CVs, and six for width/height ratio CVs. Thirteen regions in seven chromosomes were associated with two or more pod traits. Eighteen QTLs for pod traits in this study colocated with previously reported QTLs for pod and seed traits. The QTL intervals encompass gene models with homologues in other species that are involved in the control of developmental processes. These results capture the complex nature of the genetic control of snap bean pod traits and confirm the significance of genomic regions harboring overlapping QTLs identified in this and other studies. The phenotypic expression of pod traits in snap bean appears to be under the control of a few genomic regions with a strong effect with additional contributions of multiple small-effect regions. Validation of the function of the candidate genes identified in associated regions will contribute to our understanding of legume pod development.

Genome-Wide Association Study to Identify Possible Candidate Genes of Snap Bean Leaf and Pod Color.

Color can be an indicator of plant health, quality, and productivity, and is useful to researchers to understand plant nutritional content in their studies. Color may be related to chlorophyll content and photosynthetic activity and provides information for those studying diseases and mineral nutrition because every nutrient deficiency and many diseases produce symptoms that affect color. In order to identify significant loci related to both leaf and pod color in a snap bean (Phaseolus vulgaris L.) diversity panel, a genome-wide association study (GWAS) was carried out. Leaf color in one and pod traits in multiple environments were characterized using a colorimeter. L*a*b* color data were recorded and used to calculate chroma (C*) and hue angle (H°). Leaves were evaluated at three positions (lower, middle, and upper) in the canopy and both pod exterior and interior colors were obtained. GWAS was conducted using two reference genomes that represent the Andean (G19833) and Middle American (5-593) domestication centers. Narrow sense heritabilities were calculated using the mixed linear model (MLM) method in genome association and prediction integrated tool (GAPIT), and significant single nucleotide polymorphisms (SNPs) for each color parameter were obtained using the Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) GWAS model with two principal components (PCAs). In comparison to pod color traits, narrow sense heritabilities of leaf traits were low and similar for both reference genomes. Generally, narrow sense heritability for all traits was highest in the lower, followed by middle, and then upper leaf positions. Heritability for both pod interior and exterior color traits was higher using the G19833 reference genome compared to 5-593 when evaluated by year and means across years. Forty-five significant SNPs associated with leaf traits and 872 associated with pods, totaling 917 significant SNPs were identified. Only one SNP was found in common for both leaf and pod traits on Pv03 in the 5-593 reference genome. One-hundred thirteen significant SNPs, 30 in leaves and 83 in pods had phenotypic variation explained (PVE) of 10% or greater. Fourteen SNPs (four from G19833 and ten from 5-593) with ≥10 PVE%, large SNP effect, and largest p-value for L* and H° pod exterior was identified on Pv01, Pv02, Pv03, and Pv08. More SNPs were associated with pod traits than with leaf traits. The pod interior did not exhibit colors produced by anthocyanins or flavonols which allowed the differentiation of potential candidate genes associated with chloroplast and photosynthetic activity compared to the pod exterior where candidate genes related to both flavonoids and photosynthesis affected color. Several SNPs were associated with known qualitative genes including the wax pod locus (y), persistent color (pc), purple pods (V), and two genes expressed in seeds but not previously reported to affect other plant tissues (B and J). An evaluation of significant SNPs within annotated genes found a number, within a 200 kb window, involved in both flavonoid and photosynthetic biosynthetic pathways.

The Fastest and Most Reliable Identification of True Hybrids in the Genus Pisum L.

After crosses, the identification of true hybrids is not only the most important step in the initiation of a breeding program but also plays a crucial role in the improvement of hybrid varieties. However, current morphological or molecular-based hybrid identification methods are time-consuming and costly approaches that require knowledge and skill, as well as specific lab equipment. In the current study, xenia, direct or immediate effect of pollen on seeds was used to identify true hybrids in the genus Pisum L. for the first time without growing F1 plants. The current study was therefore aimed to (i) elucidate the xenia effect on seeds in intra- and interspecific crosses between P. sativum L. subsp. sativum var. sativum or var. arvense L. Poir. and its wild relatives, including P. sativum subsp. elatius (M. Bieb.) Aschers & Graebn. and P. fulvum Sibth. & Sm., and (ii) illuminate the beneficialness of the xenia effect in a practical improvement of the genus Pisum L. The pea cultivars, including P. sativum subsp. sativum var. sativum and P. sativum subsp. sativum var. arvense, were therefore crossed with P. sativum subsp. elatius and P. fulvum, and the occurrence of the xenia effect was studied on the seeds of fertilized female plants immediately after the crosses. It was concluded that using the xenia effect for the early detection of true hybrid immediately after crossing was not only the fastest, most reliable, and least expensive option as early selection criteria, but that xenia also provided information about dominant seed and pod traits after double fertilization.

Association mapping of plant structure and yield traits in faba bean (Vicia faba L.)

AbstractBackgroundFaba bean (Vicia faba L.) is an important crop with high protein content. Tens of thousands of faba bean accessions are available in germplasm collections throughout the world. Morphological characterization of these materials can enrich these collections and aid in the selection of genotypes for use in breeding programs.ResultsIn this study, 26 morphological characters were analyzed for 61 faba bean landraces and 53 cultivars over two seasons in Izmir, Turkey. The genotypes had high diversity for several yield traits including number of pods per plant, dry seed yield, and 100‐seed weight. Association mapping was conducted for the morphological characters using 651 alleles from 100 simple sequence repeat (SSR) markers and a general linear model based on the Q matrix. A false discovery rate of 0.20 was used to test the significance of marker–trait associations resulting in 75 loci detected for 20 of the morphological characters (p ≤ 0.001).ConclusionOverall, 44% of the quantitative trait loci (QTLs) were for seed traits, with 24%, 15%, and 17% of QTL identified for vegetative, inflorescence, and pod traits, respectively. The phenotypic data and marker–trait associations generated by this work can help breeding programs in the selection and improvement of faba bean.

Genetic Studies on Yield and Yield Attributing Traits in Pole Beans (Phaseolus vulgaris L.) under Lower Pulney Hills of Western Ghats

Background: In any crop improvement, hybridization among selected/chosen parents is the first foremost important step. Diversity among the genotypes is the basis for choice of parents. It requires knowledge on genetic nature of traits and such information will allow plant breeders to predict the response to selection in breeding programmes. Pole bean, a self pollinated crop, is morphologically diversity is high with distinguishable qualitative and variable quantitative traits. Methods: A field experiment was carried out at Horticultural Research Station, Tamil Nadu Agricultural University, Thadiyankudisai with 31 pole beans genotypes which were evaluated for nine characters. The experiment was laid out in a randomized block design and replicated thrice. Result: Analysis of variance revealed the significant difference among genotypes for all the studied characters. Per se performance of the 31 genotypes showed that the genotype Pallathuvaikal local performed as the best genotype for number of pods per plant, pod weight, pod yield per plant, pod yield per plot and pod yield per hectare. The traits pod length, pod girth, number of pods per plant, pod weight and yield per plant had exhibited high to medium PCV and GCV. The results of heritability and genetic advance showed that the traits pod length, number of pods per plant, pod weight, yield per plant, yield per plot and yield per hectare had exhibited high degree of heritability and genetic advance.

Genetic Analyses of Mungbean [Vigna radiata (L.) Wilczek] Breeding Traits for Selecting Superior Genotype(s) Using Multivariate and Multi-Traits Indexing Approaches.

Mungbean [Vigna radiata (L.) Wilczek] is an important food, feed, and cash crop in rice-based agricultural ecosystems in Southeast Asia and other continents. It has the potential to enhance livelihoods due to its palatability, nutritional content, and digestibility. We evaluated 166 diverse mungbean genotypes in two seasons using multivariate and multi-traits index approaches to identify superior genotypes. The total Shannon diversity index (SDI) for qualitative traits ranged from moderate for terminal leaflet shape (0.592) to high for seed colour (1.279). The analysis of variances (ANOVA) indicated a highly significant difference across the genotypes for most of the studied traits. Descriptive analyses showed high diversity among genotypes for all morphological traits. Six components with eigen values larger than one contributed 76.50% of the variability in the principal component analysis (PCA). The first three PCs accounted for the maximum 29.90%, 15.70%, and 11.20% of the total variances, respectively. Yield per plant, pod weight, hundred seed weight, pod length, days to maturity, pods per plant, harvest index, biological yield per plant, and pod per cluster contributed more to PC1 and PC2 and showed a positive association and positive direct effect on seed yield. The genotypes were grouped into seven clusters with the maximum in cluster II (34) and the minimum in cluster VII (10) along with a range of intra-cluster and inter-cluster distances of 5.15 (cluster II) to 3.60 (cluster VII) and 9.53 (between clusters II and VI) to 4.88 (clusters I and VII), suggesting extreme divergence and the possibility for use in hybridization and selection. Cluster III showed the highest yield and yield-related traits. Yield per plant positively and significantly correlated with pod traits and hundred seed weight. Depending on the multi-trait stability index (MTSI), clusters I, III, and VII might be utilized as parents in the hybridization program to generate high-yielding, disease-resistant, and small-seeded mungbean. Based on all multivariate-approaches, G45, G5, G22, G55, G143, G144, G87, G138, G110, G133, and G120 may be considered as the best parents for further breeding programs.

Taxonomic notes on the genus Brachypterum (Fabaceae: Millettieae)

Brachypterum was highly supported as a distinct genus from Derris within the tribe Millettieae by recent molecular and mophological evidence. Brachypterum pseudorobustum (basionym: Derris pseudorobusta) and Derris robusta var. assamica were originally described on fruiting collections from Northeast India, and their flowers were never described. The former species was considered be unique in having habit of scandent shrub, 15-foliolate leaves with minutely puberulous hairs, and one-winged pods usually with multiple seeds per pod. The latter taxon is still remained in Derris, although D. robusta has been accepted as Brachypterum robustum. However, our comparision of characters suggests the former species is quite similar with B. eriocarpum in various characters including its habit, leaf and pod traits, and the latter taxon most closely matches the features of Robinia pseudoacacia from the tribe Robinieae. As a result, Brachypterum pseudorobustum and Derris robusta var. assamica are both excluded from the accepted species list of Brachypterum in this study. A key to all the eleven accepted species of Brachypterum is first provided.

Characterization and evaluation of morphological and yield traits of tamarind genotypes

The evaluation of morphological and yield traits of tamarind genotypes was carried out during 2017-18 at Forest Research Station, Govinkovi, Honnali taluk, Davangere district. The experiment was laid out in randomized complete block design with 16 genotypes and three replications. Trees were 14-years-old and of grafted origin. All the morphological and yield traits showed significant difference among the selected genotypes indicating the presence of adequate variations. The genotypes recorded morphological variation in terms of tree shape (semi-circle to irregular shape), foliage arrangement (dense to sparse), flowering time (early, mid and late), stem colour (dark brown, brown and light brown), bud colour (greenish white, pink, dark pink), petal colour (yellow and pale yellow), pod colour (greyish brown, brown, light brown and dark brown), pulp colour (light brown, brown and reddish brown), pod shape (straight, slightly curved, curved and deeply curved) and pod size (very big, big, medium and small). The analysis of variance revealed significant difference with respect to tree height, stem girth, pod traits, pod yield per tree (K-9 : 12.80 kg), number of pods per tree (NTI-52 : 989.07) and pulp per cent (K-9 : 48.87). Among the 16 genotypes, the genotype K-9 was found superior with respect to pod size, pod weight, pulp weight and pod yield per tree. Genotype K-9 was found promising and due to perennial in nature further evaluation is required for stability.

Spraying sorbitol-chelated calcium affected foliar calcium absorption and promoted the yield of peanut (Arachis hypogaea L.).

The prevalent use of foliar calcium fertilizers in peanut production is inorganic, but calcium absorbed from the foliar has poor availability. Sorbitol-chelated calcium is a novel organic foliar calcium fertilizer that has rarely been studied for application in peanut production. To explore whether calcium absorption and peanut yields can be affected by foliar application of sorbitol-chelated calcium, this study conducted two field experiments using Virginia peanut (Huayu-22) in 2020 and 2021. The five spray treatments included: deionized water (CK), sorbitol (Sor), calcium nitrate (CaN), a mixture of sorbitol and calcium nitrate (SN), and sorbitol-chelated calcium (SC). The yield of peanuts treated with sorbitol-chelated calcium was increased by 12.31-16.63%, 10.22-11.83%, 6.31-9.69%, and 4.18-6.99% compared to the CK, Sor, CaN, and SN treatments, respectively. Sorbitol-chelated calcium had the lowest contact angle due to the wetting effect of sorbitol, which promoted calcium absorption by leaves. Sorbitol-chelated calcium improved the leaf calcium concentration by 13.12-19.32% and kernel calcium concentration by 6.49-8.15% compared to the CK treatment. Foliar fertilization increased the calcium concentration of each subcellular fraction of leaves and changed the distribution of calcium in mesophyll cells. This change was directly observed by transmission electron microscopy. Additionally, spraying sorbitol alone obtained similar effects to spraying calcium nitrate alone, indicating that the benefits of sorbitol itself were not negligible. The results of the principal component and correlation analysis showed that the increase in calcium concentrations and the change in calcium distribution improved the pod traits of the peanut, thus affecting the peanut yield. The above results showed that from the perspective of calcium absorption and distribution, sorbitol-chelated calcium is a more effective foliar calcium fortifier for peanuts and effectively improves peanut yields.

Genome-Wide Association Study Reveals That PvGUX1_1 Is Associated with Pod Stringlessness in Snap Bean (Phaseolus vulgaris L.).

Simple SummaryUsing 138 snap bean accessions as plant materials, we investigated their suture strings across two years. With the goal of identifying the gene(s) responsible for the formation of suture strings, we conducted a genome-wide association study. A strong association signal was found in a 266.19 kb region on Chr02. Within the region, 23 candidate genes were identified. Importantly, the sequence and gene expression of PvGUX1_1 differed significantly between sutured pods and non-sutured pods. In addition, PvGUX1_1 was also a domesticated locus that diverged from PvGUX1_2 during an early stage. The results obtained in this study can provide important information for the improvement of pod quality in snap beans.Suture strings are a particularly important pod trait that determine the quality and texture of snap beans (Phaseolus vulgaris L.). The St locus on chromosome 2 has been described as a major locus associated with suture strings. However, the gene and genetic basis underlying this locus remain unknown. Here, we investigated the suture strings of 138 snap bean accessions across two years. A total of 3.66 million single-nucleotide polymorphisms (SNPs) were obtained by deep resequencing. Based on these SNPs, we identified a strong association signal on Chr02 and a promising candidate gene, PvGUX1_1. Further analysis revealed that the 2 bp deletion in the exon of PvGUX1_1 was significantly associated with stringlessness. Comparative mapping indicated that PvGUX1_1 was a domesticated locus and diverged from PvGUX1_2 during an early stage. Our study provides important insights into the genetic mechanism of suture string formation and useful information for snap bean improvement.

A Core Set of Snap Bean Genotypes Established by Phenotyping a Large Panel Collected in Europe.

Snap beans are a group of bean cultivars grown for their edible immature pods. The objective of this work was to characterize the diversity of pod phenotypes in a snap bean panel (SBP), comprising 311 lines collected in Europe, and establish a core set (Core-SBP) with the maximum diversity of pod phenotypes. Phenotyping of the SBP was carried out over two seasons based on 14 quantitative pod dimension traits along with three qualitative traits: pod color, seed coat color, and growth habit. Phenotypes were grouped into 54 classes using a hierarchical method, and a Core-SBP with one line per phenotype class was established. A further field-based evaluation of the Core-SBP revealed higher diversity index values than those obtained for the SBP. The Core-SBP was also genotyped using 24 breeder-friendly DNA markers tagging 21 genomic regions previously associated with pod trait control. Significant marker-trait associations were found for 11 of the 21 analyzed regions as well as the locus fin. The established Core-SBP was a first attempt to classify snap bean cultivars based on pod morphology and constituted a valuable source of characteristics for future breeding programs and genetic analysis.

Identification of Finely Mapped Quantitative Trait Locus and Candidate Gene Mining for the Three-Seeded Pod Trait in Soybean.

The three-seeded pod number is an important trait that positively influences soybean yield. Soybean variety with increased three-seeded pod number contributes to the seed number/plant and higher yield. The candidate genes of the three-seeded pod may be the key for improving soybean yield. In this study, identification and validation of candidate genes for three-seeded pod has been carried out. First, a total of 36 quantitative trait locus (QTL) were detected from the investigation of recombinant inbred lines including 147 individuals derived from a cross between Charleston and Dongning 594 cultivars. Five consensus QTLs were integrated. Second, an introgressed line CSSL-182 carrying the target segment for the trait from the donor parent was selected to verify the consensus QTL based on its phenotype. Third, a secondary group was constructed by backcrossing with CSSL-182, and two QTLs were confirmed. There were a total of 162 genes in the two QTLs. The mining of candidate genes resulted in the annotation of eight genes with functions related to pod and seed sets. Finally, haplotype analysis and quantitative reverse transcriptase real-time PCR were carried to verify the candidate genes. Four of these genes had different haplotypes in the resource group, and the differences in the phenotype were highly significant. Moreover, the differences in the expression of the four genes during pod and seed development were also significant. These four genes were probably related to the development process underlying the three-seeded pod in soybean. Herein, we discuss the past and present studies related to the three-seeded pod trait in soybean.

Identification and fine genetic mapping of the golden pod gene (pv-ye) from the snap bean (Phaseolus vulgaris L.).

Using bulked segregant analysis combined with next-generation sequencing, we delimited the pv-ye gene responsible for the golden pod trait of snap bean cultivar A18-1. Sequence analysis identified Phvul.002G006200 as the candidate gene. The pod is the main edible part of snap beans (Phaseolus vulgaris L.). The commercial use of the pods is mainly affected by their color. Consumers seem to prefer golden pods. The aim of the present study was to identify the gene responsible for the golden pod trait in the snap bean. 'A18-1' (a golden bean cultivar) and 'Renaya' (a green bean cultivar) were chosen as the experimental materials. Genetic analysis indicated that a single recessive gene, pv-ye, controls the golden pod trait. A candidate region of 4.24Mb was mapped to chromosome Pv 02 using bulked-segregant analysis coupled with whole-genome sequencing. In this region, linkage analysis in an F2 population localized the pv-ye gene to an interval of 182.9 kb between the simple sequence repeat markers SSR77 and SSR93. This region comprised 16 genes (12 annotated genes from the P. vulgaris database and 4 functionally unknown genes). Combined with transcriptome sequencing results, we identified Phvul.002G006200 as the potential candidate gene for pv-ye. Sequencing of Phvul.002G006200 identified a single-nucleotide polymorphism (SNP) in pv-ye. A pair of primers covering the SNP were designed, and the fragment was sequenced to screen 1086 F2 plants with the 'A18-1' phenotype. Our findings showed that among the 1086 mapped individuals, the SNP cosegregated with the 'A18-1' phenotype. The findings presented here could form the basis to reveal the molecular mechanism of the golden pod trait in the snap bean.

Study of principal component analyses for pod traits in soybean

Yield being a complex entity influenced by several components and environments. PCA is a well-known method of dimension reduction that can be used to reduce a large set of variables to a small set that still contains most of the information in the large set (Massay, 1965 and Jolliffie, 1986). In present study, PCA preformed for pod and yield traits revealed that out of fourteen, only five principal components (PCs) exhibited more than 1.0 eigen value and showed about 70.44% total variability among the traits. PC1 showed 23.83% variability with eigen value 3.33 indicating the maximum variation in comparison to other four PCs. The PC1 was more related to traits viz., days to 50% flowering, total number of pods per plant, number of seeds per plant, biological yield per plant and seed yield per plant. Thus, PC1 allowed for simultaneous selection of yield related traits and it can be regarded as yield factor. PC2 exhibited positive effect for days to maturity, number of primary branches per plant and number of nodes per plant, The PC3 was more related to number of two seeded pods per plant, 100 seed weight and harvest index traits, whereas PC4 was more loaded with three seeded pods per plant. PC5 was more related to plant height and number of one seeded pods per plant. A high value of PC score of a particular advanced line in a particular PC denotes high value for those variables. Genotypes namely KS 103, JS 20-15, PS 1423, Cat 1957, Cat 1958, JS 20-06 and JS 20-66 can be considered an ideotype breeding material for selection and for further utilization in precise breeding programme.