Seed Coat Cracking Research Articles

Soybean Seed Coat Cracks and Green Seeds—Predisposing Conditions, Identification and Management

Seed coat cracking and green seeds threaten soybean crop production. Seed coat cracking results from a complex interplay of genetic factors, environmental stresses, and crop management practices. Green seeds, linked to water deficit, nutritional deficiencies, and environmental stresses, exhibit reduced quality and viability. The intricate relationships between seed coat integrity and seed permeability, influenced by the lignin content, porosity, and color, play a pivotal role in seed germination, storage potential, and resistance to field stresses. These issues reverberate through the soybean agricultural supply chain. Strategic interventions are crucial to address these abnormalities and ensure soybean productivity. Seed germination and vigor are reduced due to seed coat cracking and green seeds, undermining food security and necessitating additional resources for disease management. The occurrence and identification of green seeds and seeds with cracks in the seed coat were also reported by identifying the genes and QTLs (quantitative trait loci) associated with these characteristics. Herbicides, commonly used in weed management, may offer a strategic approach to mitigating seed coat cracking and green seed occurrence. Understanding the complex interactions between the genetics, environmental factors, and management practices influencing seed abnormalities is essential as global climate change intensifies. This review emphasizes the need for integrated strategies, balanced plant nutrition, and cohesive phytosanitary management to mainly alleviate seed coat cracking and greenish occurrences in soybeans and other plant species.

Metabolomics based on GC-MS revealed hub metabolites of pecan seeds germinating at different temperatures

BackgroundAs an important plant source of food and edible oils, pecans are rich in metabolites. Few studies have focused on metabolites involved in pecan seed germination at different temperatures.ResultsIn our study, we germinated pecan seeds at different temperatures and found that, the germination rate and water content were highest at 30°C. It was found that the radicle of pecan seeds could sense seed coat cracking by observing the microstructure and cell ultra-structure of the seeds at the early stage of germination. We compared the metabolomes of seeds at different temperatures with different germination processes. A total of 349 metabolites were identified, including 138 primary metabolites and 211 secondary metabolites. KEGG enrichment analysis indicated that the differential metabolites were mainly enriched in the metabolic pathways, amino acid synthesis pathways and ABC transporters. Using weighted gene co-expression network analysis (WGCNA), three modules of closely related metabolites were identified. In the brown module, most of hub metabolites were amino substances, whereas in the blue module, many hub metabolites were sugars.ConclusionsAmino acids and carbohydrates play an important role in pecan seed germination. Differential metaboliteanalysis showed that 30°C was the temperature at which metabolites differed most significantly. This study provides useful information for further research on the seedling establishment of pecan seeds.

High-density linkage map reveals QTL for Type-I seed coat cracking in RIL population of soybean [Glycine max (L.) Merr.

Seed coat cracking (SCC), particularly the Type-I irregular cracking, is critical in determining the quality of appearance and commercial value of soybean seeds. The objective of this study was to identify the quantitative trait loci (QTLs) for SCC with high-density genetic map. One hundred sixty-seven recombinant inbred lines (RILs) developed from a cross between Uram (SCC-resistant) and Chamol (SCC-susceptible) were evaluated for SCC over 2 years (2016–2017). The QTL analysis identified 12 QTLs located on chromosomes 2 (D1b), 6 (C2), 8 (A2), 9 (K), 10 (O), 12 (H), 19 (L), and 20 (I). Out of the 12 QTLs, qSC2-1, qSC9, SC10-1, qSC10-2, and qSC12 were novel QTLs and the other seven QTLs (qSC2-2, qSC2-3, qSC6, qSC8, qSC19-1, qSC19-2, and qSC20) were found to co-localize with the previously identified QTLs. The mean SCC of the RILs of early maturity group was significantly higher than that of the late maturity group, suggesting an association between SCC and maturity loci. In addition, although 10 QTLs were distantly located from the maturity loci (E1, E3, E4, E7, and E10), qSC10-1 and qSC10-2 co-localized with the maturity loci E2. The results obtained in this study provide useful genetic information on SCC which could be used in the SCC breeding programs.

Identification and validation of major QTLs associated with low seed coat deficiency of natto soybean seeds (Glycine max L.)

Key messageTwo 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.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.

黒ダイズ品種「丹波黒」の皮切れ粒に由来するセル成型苗の損傷

黒ダイズ品種「丹波黒」の皮切れ粒に由来するセル成型苗の損傷

A QTL associated with high seed coat cracking rate of a leading Japanese soybean variety

Seed coat cracking in soybeans [Glycine max (L). Merr.] leads to commercial and agronomic losses. The Japanese elite soybean cultivar ‘Fukuyutaka’ is often used as a parent for breeding, but its high rate of seed coat cracking is an obstacle to its further use in breeding programs. To establish a DNA marker-assisted selection system for seed coat cracking, genetic factors related to high rates of seed coat cracking were surveyed, and a quantitative trait locus (QTL) with a stable effect on seed coat cracking in both years of a two-year replication experiment was detected on chromosome 20. Comparison of a set of near-isogenic lines (NILs) around this locus verified that the presence of the ‘Fukuyutaka’ allele significantly increased seed coat cracking in the kernel. The locus is located in a genomic region spanning 3.2 Mb. Marker-assisted selection for the locus will improve the selection efficiency of ‘Fukuyutaka’-derived breeding populations.

Seed Coat Cracking in a Soybean Cultivar “Satonohohoemi” and Effects of Planting Time on Its Occurrence

Seed Coat Cracking in a Soybean Cultivar “Satonohohoemi” and Effects of Planting Time on Its Occurrence

大豆生育期の低温処理が品質に及ぼす影響 : 臍周辺の着色と種皮の裂皮(年次会講演要旨)

大豆生育期の低温処理が品質に及ぼす影響 : 臍周辺の着色と種皮の裂皮(年次会講演要旨)

Transcriptome Analysis of a New Peanut Seed Coat Mutant for the Physiological Regulatory Mechanism Involved in Seed Coat Cracking and Pigmentation.

Seed-coat cracking and undesirable color of seed coat highly affects external appearance and commercial value of peanuts (Arachis hypogaea L.). With an objective to find genetic solution to the above problems, a peanut mutant with cracking and brown colored seed coat (testa) was identified from an EMS treated mutant population and designated as “peanut seed coat crack and brown color mutant line (pscb).” The seed coat weight of the mutant was almost twice of the wild type, and the germination time was significantly shorter than wild type. Further, the mutant had lower level of lignin, anthocyanin, proanthocyanidin content, and highly increased level of melanin content as compared to wild type. Using RNA-Seq, we examined the seed coat transcriptome in three stages of seed development in the wild type and the pscb mutant. The RNA-Seq analysis revealed presence of highly differentially expressed phenylpropanoid and flavonoid pathway genes in all the three seed development stages, especially at 40 days after flowering (DAF40). Also, the expression of polyphenol oxidases and peroxidase were found to be activated significantly especially in the late seed developmental stage. The genome-wide comparative study of the expression profiles revealed 62 differentially expressed genes common across all the three stages. By analyzing the expression patterns and the sequences of the common differentially expressed genes of the three stages, three candidate genes namely c36498_g1 (CCoAOMT1), c40902_g2 (kinesin), and c33560_g1 (MYB3) were identified responsible for seed-coat cracking and brown color phenotype. Therefore, this study not only provided candidate genes but also provided greater insights and molecular genetic control of peanut seed-coat cracking and color variation. The information generated in this study will facilitate further identification of causal gene and diagnostic markers for breeding improved peanut varieties with smooth and desirable seed coat color.

GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean.

Loss of seed-coat impermeability was essential in the domestication of many leguminous crops to promote the production of their highly nutritious seeds. Here we show that seed-coat impermeability in wild soybean is controlled by a single gene, GmHs1-1, which encodes a calcineurin-like metallophosphoesterase transmembrane protein. GmHs1-1 is primarily expressed in the Malpighian layer of the seed coat and is associated with calcium content. The transition from impermeability to permeability in domesticated soybean was caused by artificial selection of a point mutation in GmHs1-1. Interestingly, a number of soybean landraces evaded selection for permeability because of an alternative selection for seed-coat cracking that also enables seed imbibition. Despite the single origin of the mutant allele Gmhs1-1, the distribution pattern of allelic variants in the context of soybean population structure and the detected signature of genomic introgression between wild and cultivated soybeans suggest that Gmhs1-1 may have experienced reselection for seed-coat permeability.

Effect of fruit size on the growth and development of Andean blueberry (Vaccinium meridionale Swartz) seedlings from four locations in the Colombian Andes

Andean blueberry propagation is done with wild plants and there is an absence of knowledge for the agronomical potential of the available materials for sexual propagation. Therefore, developing a propagation protocol that provides technical information for field growers is needed. The present paper aimed to evaluate the effect of the size of the fruits that were used to extract the seeds on the growth and development of Andean blueberry plants during the germination and nursery stages, comparing fruits from four different regions of Colombia: Antioquia, Cauca, Cundinamarca and Boyaca. During the germination stage, seeds from Antioquia and Cauca showed the best results with germination rates close to 90% and reached important physiological events, such as seed coat cracking and radicle extension earlier than seeds from Boyaca and Cundinamarca. In the nursery stage, fruit size significantly affected the growth variables, such as plant height and leaf length, in all the different seed origins. Seedlings from Boyaca showed better results for growth and development after transplanting, as indicated by a higher amount of leaves and presence of basal branching, followed by seedlings from Cauca, Cundinamarca and Antioquia, which showed delayed phenological events.

Development and validation of DNA markers linked to Sdvy-1, a common bean gene conferring resistance to the yellowing strain of Soybean dwarf virus.

The yellowing strain of Soybean dwarf virus (SbDV-YS) causes yellowing and yield loss in common bean (Phaseolus vulgaris). The most effective control is achieved through breeding for resistance. An indeterminate climbing cultivar with a white seed coat, ‘Oofuku’, is resistant to SbDV-YS in inoculation tests. We crossed ‘Oofuku’ with an elite cultivar, ‘Taisho-Kintoki’, which is SbDV-YS-susceptible, determinate dwarf with a red-purple seed coat, and performed amplified-fragment-length polymorphism analysis of F3 lines. From nucleotide sequences of the resistant-specific fragments and their flanking regions, we developed five DNA markers, of which DV86, DV386, and DV398 were closely linked to Sdvy-1, a resistance gene. Using the markers, we developed ‘Toiku-B79’ and ‘Toiku-B80’, the near-isogenic lines (NILs) incorporating Sdvy-1 in the background of ‘Taisho-Kintoki’. The NILs had similar growth habit, maturity date and seed shape to those of ‘Taisho-Kintoki’. The quality of boiled beans was also similar, except that the NILs had more seed coat cracking than ‘Taisho-Kintoki’. The NILs showed no SbDV-YS infection in inoculation tests. We suggest that Sdvy-1 is a useful source of SbDV-YS resistance in common bean.

Mapping QTLs with epistatic effects and QTL-by-environment interactions for seed coat cracking in soybeans

Seed coat cracking (SCC) consists of irregular cracks on the surface of seed coat, giving rise to serious effects on the seed quality in soybeans. However, breeding to achieve resistance to SCC has been an arduous task due to the complicated genetic behavior and environmental interactions. Thus, this study aims to map quantitative trait loci (QTLs) controlling irregular SCC in soybeans and to study QTL-by-environment interactions. QTL analysis was conducted using an RIL population derived from Keunolkong × Sinpaldalkong. The SCC was determined at natural conditions and calculated three times by counting cracked seeds with a 100 seeds per plant basis. In the four environments, a total of 10 QTLs with additive effects were identified. Among them, three QTLs (qSCC2-1, qSCC9, and qSCC20) located on chromosomes 2, 9, and 20 showed main-additive effects explaining 9.5–19.4 % of phenotypic variances in two environments. Across environments, seven additive QTLs, four additive × environment (AE) interactions, and two pairs of epistatic QTLs and epistasis × environment interactions were identified for SCC. Similar to the results in individual environments, two major QTLs (qSCC2-1 and qSCC9) showed additive main effects explaining 10.5 and 6.5 % of phenotypic variances, respectively and significant AE interaction in 2006 Suwon. The total QTLs explained 48.0 % of the phenotypic variation, with additive effects of 33.8 %, epistatic effects of 7.6 %, and AE and AAE of 6.6 %. All in all, these results showed that both additive effects and AE interactions can serve as important genetic basis for SCC.

Inheritance of Natural Seed-Coat Cracking in Chickpea

A spontaneous mutant with natural seed-coat cracking, designated "cracked seed-coat mutant (CSM)," was identified in chickpea (Cicer arietinum L.) from an F(2) population of a cross ICRISAT chickpea (ICC) 10301 × ICC 12430. The extent of seed-coat cracking (SCC) varied widely from a minute to several wide cracks. Seed coats showed cracks before seeds were fully developed and the plants had reached physiological maturity. However, seed-coat cracks were most visible on dry matured seeds, particularly in desi types. Two loci (Scc-1 and Scc-2) that controlled SCC were identified. F(1) plants from the crosses of CSM with desi genotypes produced seeds with no SCC, whereas F(1) plants from the crosses of CSM with kabuli genotypes produced seeds with SCC. F(2) segregation followed 13:3 and 7:9 ratios for plants without SCC and with SCC in CSM × Desi and CSM × Kabuli crosses, respectively. Three alleles were identified at the first locus (Scc-1) from CSM (Scc-1 (c)), desi (Scc-1 (d)), and kabuli (Scc-1 (k)) types, with the dominance relationship being Scc-1 (d) > Scc-1 (c) > Scc-1 ( k ). At the second locus (Scc-2), CSM had the dominant allele (Scc-2), whereas both desi and kabuli types had the recessive allele (scc-2). The SCC trait showed no linkage with leaf type (pinnate vs. simple) and flower color (pink vs. white) and had no adverse effects on grain yield. The SCC trait may facilitate dehulling and preparation of splits (dal), but the cracked seed would be prone to damage by insect pests and unfavorable moisture conditions.

黒ダイズ「丹波黒」における裂皮発生と種皮の形態的特徴との関係

黒ダイズ「丹波黒」における裂皮発生と種皮の形態的特徴との関係

黒ダイズ「丹波黒」子実の生長と裂皮発生について

黒ダイズ「丹波黒」子実の生長と裂皮発生について

QTL Analysis of Seed Coat Cracking in Soybean

The seed coat of soybean [Glycine max (L.) Merr.] cracks under field conditions. This study was conducted to investigate the genetic basis of seed coat cracking using DNA markers. Recombinant inbred lines (RILs) were developed from a cross between a sensitive cv. Nasushirome and a tolerant cv. Enrei. Ninety‐five F6 RILs (2006) and 92 F7 RILs (2007) with an average of 24 plants per line were grown in the field. Seed coat cracking was promoted by removing the upper 50% of pods at 40 d after anthesis. The degree of cracking of each seed was scored by a cracking index (not cracked, 0, to severely cracked, 4). Cracking index was averaged per plant and, subsequently, per line (average cracking index, ACI). Linkage mapping was performed using 114 simple sequence repeat markers and one morphological trait. The markers were associated with 18 linkage groups spanning 1232 cM. Two quantitative trait loci (QTL) for ACI, cr1 in molecular linkage group (MLG) D1b and cr2 in MLG M, were identified. The cr2 QTL was detected only in the F6 generation, whereas cr1 was identified across years and generations. The cr1 had a logarithm of odds score of 4.78 (F6) and 4.77 (F7), accounting for 27.2 (F6) and 23.5% (F7) of phenotypic variation. The cr1 was not associated with seed size or maturity in F8 near‐isogenic lines. Therefore, markers around the QTL may be useful for breeding to reduce cracking symptoms without altering seed size or maturity.

Temperature and humidity for air drying of soyabeans (Part 1). Theory and testing of seed coat cracking and occurrence of swelling.

Temperature and humidity for air drying of soyabeans (Part 1). Theory and testing of seed coat cracking and occurrence of swelling.

Effect of Desiccation with Silica Gel on TTC Staining, Germination, Vigor and Seedcoat Cracking in Soybean Seeds

Effect of Desiccation with Silica Gel on TTC Staining, Germination, Vigor and Seedcoat Cracking in Soybean Seeds

2008年兵庫県産黒大豆「丹波黒」の裂皮について

2008年兵庫県産黒大豆「丹波黒」の裂皮について