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Key message Two major QTLs associated with low seed coat deficiency of soybean seeds were identified in two biparental populations, and three SNP markers were validated to assist low-SCD natto soybean breeding selection. Abstract Soybean seed coat deficiency (SCD), known as seed coat cracking during soaking in the natto production process, is problematic because split or broken beans clog production lines and increases production costs. Development of natto soybean cultivars with low SCD is crucial to support the growth of the natto industry. Unfortunately, information on the genetic control of SCD in soybean, which is desperately needed to facilitate breeding selection, remains sparse. In this study, two F2 populations derived from V11-0883 × V12-1626 (Pop 1) and V11-0883 × V12-1885 (Pop 2) were developed and genotyped with BARCSoySNP6K Beadchips and F2-derived lines were evaluated for SCD in three consecutive years (2016–2018) in order to identify quantitative trait loci (QTLs) associated with low SCD in soybean. A total of 17 QTLs underlying SCD were identified in two populations. Among these, two major and stable QTLs, qSCD15 on chromosome 15 and qSCD20 on chromosome 20, were detected across multiple years. These QTLs explained up to 30.3% of the phenotypic variation for SCD in Pop 1 and 6.1% in Pop 2 across years. Three SNP markers associated with the qSCD20 were validated in additional four biparental populations. The average selection efficiency of low-SCD soybean was 77% based on two tightly linked markers, Gm20_34626867 and Gm20_34942502, and 64% based on the marker Gm20_35625615. The novel and stable QTLs identified in this study will facilitate elucidation of the genetic mechanism controlling SCD in soybean, and the markers will significantly accelerate breeding for low-SCD soybean through marker-assisted selection.

Orphan crops, which include many of the tropical fruit species used in the juice industry, lack genomic resources and breeding efforts. Typical of this dilemma is the lack of commercial cultivars of purple passion fruit, Passiflora edulis f. edulis, and of information on the genetic resources of its substantial semiwild gene pool. In this study, we develop single-nucleotide polymorphism (SNP) markers for the species and show that the genetic diversity of this fruit crop has been reduced because of selection for cultivated genotypes compared to the semiwild landraces in its center of diversity. A specific objective of the present study was to determine the genetic diversity of cultivars, genebank accession, and landraces through genotyping by sequencing (GBS) and to conduct molecular evaluation of a broad collection for the species P. edulis from a source country, Colombia. We included control genotypes of yellow passion fruit, P. edulis f. flavicarpa. The goal was to evaluate differences between fruit types and compare landraces and genebank accessions from in situ accessions collected from farmers. In total, 3820 SNPs were identified as informative for this diversity study. However, the majority distinguished yellow and purple passion fruit, with 966 SNPs useful in purple passion fruits alone. In the population structure analysis, purple passion fruits were very distinct from the yellow ones. The results for purple passion fruits alone showed reduced diversity for the commercial cultivars while highlighting the higher diversity found among landraces from wild or semi-wild conditions. These landraces had higher heterozygosity, polymorphism, and overall genetic diversity. The implications for genetics and breeding as well as evolution and ecology of purple passion fruits based on the extant landrace diversity are discussed with consideration of manual or pollinator-assisted hybridization of this species.

Hydrangea (Hydrangea macrophylla) is an important ornamental crop that has been cultivated for more than 300 years. Despite the economic importance, genetic studies for hydrangea have been limited by the lack of genetic resources. Genetic linkage maps and subsequent trait mapping are essential tools to identify and make markers available for marker-assisted breeding. A transcriptomic study was performed on two important cultivars, Veitchii and Endless Summer, to discover simple sequence repeat (SSR) markers and an F1 population based on the cross ‘Veitchii’ × ‘Endless Summer’ was established for genetic linkage map construction. Genotyping by sequencing (GBS) was performed on the mapping population along with SSR genotyping. From an analysis of 42,682 putative transcripts, 8780 SSRs were identified and 1535 were validated in the mapping parents. A total of 267 polymorphic SSRs were selected for linkage map construction. The GBS yielded 3923 high quality single nucleotide polymorphisms (SNPs) in the mapping population, resulting in a total of 4190 markers that were used to generate maps for each parent and a consensus map. The consensus linkage map contained 1767 positioned markers (146 SSRs and 1621 SNPs), spanned 1383.4 centiMorgans (cM), and was comprised of 18 linkage groups, with an average mapping interval of 0.8 cM. The transcriptome information and large-scale marker development in this study greatly expanded the genetic resources that are available for hydrangea. The high-density genetic linkage maps presented here will serve as an important foundation for quantitative trait loci mapping, map-based gene cloning, and marker-assisted selection of H. macrophylla.

The pea (Pisum sativum L.) is one of the most important crops in temperate agriculture around the world. In the tropics, highland production is also common with multiple harvests of nearly mature seeds from climbing plant types on trellises. While the leafless variant caused by the afila gene is widely used in developing row-cropped field peas in Europe, its use for trellised garden peas has not been reported. In this study we describe a pea breeding program for a high-elevation tropical environment in the Department of Nari&ntilde, o in Colombia, where over 16,000 hectares of the crop are produced. The most widespread climbing varieties in the region are &lsquo, Andina&rsquo, and &lsquo, Sindamanoy&rsquo, both of which have high-biomass architecture with abundant foliage. They are prone to many diseases, but preferred by farmers given their long production season. This plant type is expensive to trellis, with wooden posts and plastic strings used for vine staking constituting 52% of production costs. The afila trait could reduce these costs by creating interlocking plants as they do in field peas. Therefore, our goal for this research was to develop a rapid breeding method to introduce the recessive afila gene, which replaces leaves with tendrils, into the two commercial varieties used as recurrent parents (RPs) with three donor parents (DPs)&mdash, &lsquo, Dove&rsquo, ILS3575&rsquo, ILS3568&rsquo, &mdash, and to measure the effect on plant height (PH) and yield potential. Our hypothesis was that the afila gene would not cause linkage drag while obtaining a leafless climbing pea variety. Backcrossing was conducted without selfing for two generations and plants were selected to recover recurrent parent characteristics. Chi-square tests showed a ratio of 15 normal leaved to one afila leaved in the BC2F2 plants, and 31:1 in the BC2F3 generation. Selecting in the last of these generations permitted a discovery of tall climbing plants that were similar to those preferred commercially, but with the stable leafless afila. The method saved two seasons compared to the traditional method of progeny testing before each backcross cycle, the peas reached the BC2F2 generation in five seasons and the BC3F2 in seven seasons. This is advantageous with trellised peas that normally require half a year to reach maturity. Leafless garden peas containing the afila gene were of the same height as recurrent parents and, by the third backcross, were equally productive, without the high biomass found in the traditional donor varieties. The value of the afila gene and the direct backcrossing scheme is discussed in terms of garden pea improvement and crop breeding.

Inflorescence type and remontancy are two valuable traits in bigleaf hydrangea (Hydrangea macrophyllaL.) and both are recessively inherited. Molecular marker-assisted selection (MAS) can greatly reduce the time necessary to breed cultivars with desired traits. In this study, a genome-wide association study (GWAS) using 5803 single-nucleotide polymorphisms (SNPs) was performed using a panel of 82 bigleaf hydrangea cultivars. One SNP locus (Hy_CAPS_Inflo) associated with inflorescence type was identified with general linear model (GLM) and mixed linear model (MLM) methods that explained 65.5% and 36.1% of the phenotypic variations, respectively. Twenty-three SNPs associated with remontancy were detected in GLM whereas no SNP was detected in MLM. The SNP locus (Hy_CAPS_Inflo) was converted to a cleaved amplified polymorphic sequence (CAPS) marker that showed absolute identification accuracy (100%) of inflorescence type in a validation panel consisting of eighteenH. macrophyllacultivars. The SNP was investigated in 341 F1progenies using genotyping by sequencing (GBS) and co-segregated with inflorescence type (χ2 = 0.12;P = 0.73). The SNP was subsequently used for breeding selection using kompetitive allele specific PCR (KASP) technology. Future directions for the use of genomics and MAS in hydrangea breeding improvement are discussed. The results presented in this study provide insights for further research on understanding genetic mechanisms behind inflorescence type and remontancy inH. macrophylla. The CAPS and KASP markers developed here will be immediately useful for applying MAS to accelerate breeding improvement in hydrangea.

Plant peroxidases (POXs) are one of the most important redox enzymes in the defense responses. However, the large number of different plant POX genes makes it necessary to carefully confirm the function of each paralogous POX gene in specific tissues and disease interactions. Fusarium wilt is a devastating disease of common bean caused by Fusarium oxysporum f. sp. phaseoli. In this study, we evaluated a peroxidase gene, PvPOX1, from a resistant common bean genotype, CAAS260205 and provided direct evidence for PvPOX1's role in resistance by transforming the resistant allele into a susceptible common bean genotype, BRB130, via hairy root transformation using Agrobacterium rhizogenes. Analysis of PvPOX1 gene over-expressing hairy roots showed it increased resistance to Fusarium wilt both in the roots and the rest of transgenic plants. Meanwhile, the PvPOX1 expressive level, the peroxidase activity and hydrogen peroxide (H2O2) accumulation were also enhanced in the interaction. The result showed that the PvPOX1 gene played an essential role in Fusarium wilt resistance through the occurrence of reactive oxygen species (ROS) induced hypersensitive response. Therefore, PvPOX1 expression was proven to be a valuable gene for further analysis which can strengthen host defense response against Fusarium wilt through a ROS activated resistance mechanism.

CHX had remarkable inhibition on P. edulis photosynthesis, and the reflectance indexes and F 685 / F 735 had the potential value for quantifying the effects of antibiotics on trees. To reveal the effects of antibiotics on photosynthesis and provide help for remote sensing the influence of antibiotics on trees, we investigated the effects of cycloheximide (CHX) on Phyllostachys edulis. In CHX treatment, the photosynthetic pigment content in P. edulis was decreased markedly, which led to the increase in the reflectance spectra in visible region. CHX reduced the donor side and acceptor side of photosystem II (PSII), density of reaction centers, quantum production and electron transport in PSII, and raised the dissipation of absorbed light energy. Besides the dissipation, the absorbed light energy can be emitted as fluorescence with two main peaks in the red (685 nm) and far-red (735 nm) region, respectively. In 0.50 mM CHX treatment, a significant decline in the height and area of the peak at 685 nm might result from Chl loss reducing the light absorption and lower photochemical reaction in PSII. When fourth derivative analysis of fluorescence emission spectra was performed, the changes of the peaks at 718, 735 and 750 nm might result from the decline of absorbed solar radiation caused by the reduced pigment content and/or the damages to the PSI. In CHX treatment, a remarkable increase in intercellular CO2 concentrations and light compensation point and decrease in light saturation point demonstrated that the CO2 assimilation ability was decreased. Those results suggested that the photosynthesis in trees can be reduced after they were watered with wastewater containing CHX. The reflectance indexes and F 685/F 735 (H 685/H 735 and A 685/A 735) were markedly affected by CHX, demonstrating that they had the potential value for quantifying the effects of antibiotics on trees.

The genotyping by sequencing (GBS) method has become a molecular marker technology of choice for many crop plants because of its simultaneous discovery and evaluation of a large number of single nucleotide polymorphisms (SNPs) and utility for germplasm characterization. Genome representation and complexity reduction are the basis for GBS fingerprinting and can vary by species based on genome size and other sequence characteristics. Grain amaranths are a set of three species that were domesticated in the New World to be high protein, pseudo-cereal grain crops. The goal of this research was to employ the GBS technique for diversity evaluation in grain amaranth accessions and close relatives from six Amaranthus species and determine genetic differences and similarities between groupings. A total of 10,668 SNPs were discovered in 94 amaranth accessions with ApeKI complexity reduction and 10X genome coverage Illumina sequencing. The majority of the SNPs were species specific with 4,568 and 3,082 for the two grain amaranths originating in Central America Amaranthus cruentus and A. hypochondriacus and 3,284 found amongst both A. caudatus, originally domesticated in South America, and its close relative, A. quitensis. The distance matrix based on shared alleles provided information on the close relationships of the two cultivated Central American species with each other and of the wild and cultivated South American species with each other, as distinguished from the outgroup with two wild species, A. powellii and A. retroflexus. The GBS data also distinguished admixture between each pair of species and the geographical origins and seed colors of the accessions. The SNPs we discovered here can be used for marker development for future amaranth study.

Nutrient transport to grain legume seeds is not well studied and can benefit from modern methods of elemental analysis including spectroscopic techniques. Some cations such as potassium (K) and magnesium (Mg) are needed for plant physiological purposes. Meanwhile, some minerals such as copper (Cu), iron (Fe), molybdenum (Mo) and zinc (Zn) are important micronutrients. Phosphorus (P) is rich in legumes, while sulfur (S) concentration is related to essential amino acids. In this research, the goal was to analyze a genetic mapping population of common bean (Phaseolus vulgaris L.) with inductively coupled plasma (ICP) spectrophotometry to determine concentrations of and to discover quantitative trait loci (QTL) for 15 elements in ground flour of whole seeds. The population was grown in randomized complete block design experiments that had been used before to analyze Fe and Zn. A total of 21 QTL were identified for 9 additional elements, of which four QTL were found for Cu followed by three each for Mg, Mn and P. Fewer QTL were found for K, Na and S. Boron (B) and calcium (Ca) had only one QTL each. The utility of the QTL for breeding adaptation to element deficient soils and association with previously discovered nutritional loci are discussed.

Legumes are the second largest plant family on earth and arguably the second group of importance to current and past agricultural systems and human nutrition. Despite differences among legumes, their variability as early, medium, to late maturity annual crops that fix nitrogen and survive shading by larger adjacent plants, makes them very versatile in agronomics and horticultural cropping systems. In this chapter, we describe the importance of four vegetable legumes (garden peas, purple-hulled peas, snap beans, and yard-long beans) and a range of more minor legume crops as vegetables in today’s world. Each crop is highlighted for its value in the local diets of peoples of different regions and the cropping systems to which they belong. We follow this by providing a large number of examples where vegetable and non-vegetable legumes can be used as intercrops between cereal crops such as corn or sorghum, between vegetables from the tomato/pepper and eggplant or cabbage/broccoli and cauliflower family or fruit tree seedlings and saplings that are being established. All of this shows that legumes are an amazingly diverse group of vegetable species which are advantageous to intensive horticultural systems.