Genetic analysis of soybean hard seededness with molecular markers

Research advances on the hard seededness trait of soybean and the underlying regulatory mechanisms

Soybean is one of the world's most economically significant crops and is widely utilized as an essential source of vegetable protein and edible oil. Cultivated soybean is domesticated from its annual counterpart, wild soybean, which is considered valuable germplasm for soybean breeding. However, wild soybean accessions generally produce seeds with impermeable coats, a trait known as hard seededness (HS), which is beneficial for long-term seed survival but is undesirable for the uniform water absorption and germination of seeds, thus limiting the utilization of wild soybeans in breeding. In addition, moderate HS can isolate the embryo from the surrounding environment and is thus beneficial for long-term seed storage and germplasm preservation. The HS trait is primarily associated with the structure and chemical composition of the seed coat. Moreover, its development is also influenced by various environmental conditions, such as water and temperature. Genetic analysis has revealed that HS of soybean is a complex quantitative trait controlled by multiple genes or minor quantitative trait loci (QTL), with many QTLs and several causal genes currently identified. Investigating the physiological and molecular mechanisms underlying this trait is crucial for soybean breeding, production, and food processing. For this article, the literature was reviewed and condensed to create a well-rounded picture of the current understanding of internal and external factors, QTLs, causal genes, and the regulatory mechanisms related to the HS of soybean, with the aim of providing reference for future research and utilization of this trait.

Genetic analysis and QTL mapping of seed hardness trait in a soybean (Glycine max) recombinant inbred line (RIL) population

Seed hardness is a critical quality trait impacting both the suitability of soybeans for consumption and their processing. The primary objective of this study was to explore the genetic foundations underlying seed hardness in soybeans. A 234 recombinant inbred line (RIL) population was evaluated for seed hardness across three years (2015 in Gansu, 2016, and 2017 in Hainan). Notably, the parent varieties, Zhonghuang35 and Jindou21, displayed significant differences in seed hardness. Also, the RIL population exhibited a wide range of genetic variation in seed hardness, with coefficients of variation between 70.53 % and 94.94 %. The frequency distribution of this trait conformed to a relatively normal distribution, making it suitable for QTL analysis. Six QTLs associated with seed hardness were identified with three located on chromosome 2 and three on chromosome 16. The major QTL, qHS-2-1, consistently exhibited the highest percentage of PVE and LOD in Gansu 2015, Hainan 2016, and Hainan 2017, suggesting its central role in determining seed hardness. Further investigation revealed four genes within the qHS-2-1 interval potentially related to seed hardness. GO enrichment analysis provided insights into their functions, including factors such as Glyma.02G307000, a pectin lyase-like superfamily protein, which could influence seed hardness through its role in pectin lyase enzyme activity. Expression analysis of these candidate genes demonstrated significant differences between the two parent varieties, further highlighting their potential role in seed coat hardness. This study offers valuable insights into the genetic mechanisms governing soybean seed coat hardness, providing a foundation for future research and crop improvement efforts.

Current overview on the genetic basis of key genes involved in soybean domestication

Modern crops were created through the domestication and genetic introgression of wild relatives and adaptive differentiation in new environments. Identifying the domestication-related genes and unveiling their molecular diversity provide clues for understanding how the domesticated variants were selected by ancient people, elucidating how and where these crops were domesticated. Molecular genetics and genomics have explored some domestication-related genes in soybean (Glycine max). Here, we summarize recent studies about the quantitative trait locus (QTL) and genes involved in the domestication traits, introduce the functions of these genes, clarify which alleles of domesticated genes were selected during domestication. A deeper understanding of soybean domestication could help to break the bottleneck of modern breeding by highlighting unused genetic diversity not selected in the original domestication process, as well as highlighting promising new avenues for the identification and research of important agronomic traits among different crop species.

Genetics and mapping of seed coat impermeability in soybean using inter-specific populations

Seed coat impermeability (SCI) in soybean is associated with seed viability under storage and quality of processed products. Understanding genetics and identification of linked molecular markers would facilitate need-based utilization of seed coat impermeability. Two impermeable wild type (G. soja Sieb. and Zucc.) accessions viz. PI 424079 and PI 136620 were crossed with a permeable cultivated (G. max) variety JS335 to generate the mapping populations. Genetic analysis of the F_1:2 and F_2:3 seeds of the crosses indicated that SCI is controlled by a single gene/major QTL, and impermeability is dominant over permeability. Presence of seeds with intermediate permeability indicated role of some minor genes/QTLs. A set of 204 inter-specific recombinant inbred line (RILs) (F₇) was used to map SCI with 207 SSR markers. Phenotyping through rapid imbibition approach (seed imbibition for 6 h), seven QTLs were mapped on chromosomes (Chrs.) 2, 5, 12, 13 and 16 in the seeds stored for 1-3 years, while through slow imbibition method (seed imbibition for 7 days), five QTLs were mapped on Chrs. 2, 9, 10 and 20. Phenotypic variation explained (PVE) by the QTLs ranged from 5.96 to 39.67%. Two major and stable QTLs viz., qScI-h2-1 and qScI-h2-2 that mapped in tandem on Chr.2 jointly explained 43.09-62.92% of the variations in impermeability. Seven minor QTLs identified here were novel and two (qScI-h5, and qScI-h16) were consistent. It is the first report of mapping impermeability using two imbibition approaches together in 200 plus inter-specific RILs in soybean. The study will pave the way for developing genotypes with restricted permeability, enhanced seed viability, and improved seeds quality.

Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

BACKGROUND

Water permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. Moreover, the physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. Thus, to underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation.

RESULTS

In the present study, we have analyzed genomic variation between cultivated soybean and its wild progenitor with implications on seed permeability, a trait related to seed storability. Whole genome resequencing of G.max and G. soja, identified SNPs and InDels which were further characterized on the basis of their genomic location and impact on gene expression. Chromosomal density distribution of the variation was assessed across the genome and genes carrying SNPs and InDels were characterized into different metabolic pathways. Seed hardiness is a complex trait that is affected by the allelic constitution of a genetic locus as well as by a tricky web of plant hormone interactions. Seven genes that hold a probable role in the determination of seed permeability were selected and their expression differences at different stages of water imbibition were analyzed. Variant interaction network derived 205 downstream interacting partners of 7 genes confirmed their role in seed related traits. Interestingly, genes encoding for Type I- Inositol polyphosphate 5 phosphatase1 and E3 Ubiquitin ligase could differentiate parental genotypes, revealed protein conformational deformations and were found to segregate among RILs in coherence with their permeability scores. The 2 identified genes, thus showed a preliminary association with the desirable permeability characteristics.

CONCLUSION

In the light of above outcomes, 2 genes were identified that revealed preliminary, but a relevant association with soybean seed permeability trait and hence could serve as a primary material for understanding the molecular pathways controlling seed permeability traits in soybean.

QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding

Food legumes play an important role in attaining both food and nutritional security along with sustainable agricultural production for the well-being of humans globally. The various traits of economic importance in legume crops are complex and quantitative in nature, which are governed by quantitative trait loci (QTLs). Mapping of quantitative traits is a tedious and costly process, however, a large number of QTLs has been mapped in soybean for various traits albeit their utilization in breeding programmes is poorly reported. For their effective use in breeding programme it is imperative to narrow down the confidence interval of QTLs, to identify the underlying genes, and most importantly allelic characterization of these genes for identifying superior variants. In the field of functional genomics, especially in the identification and characterization of gene responsible for quantitative traits, soybean is far ahead from other legume crops. The availability of genic information about quantitative traits is more significant because it is easy and effective to identify homologs than identifying shared syntenic regions in other crop species. In soybean, genes underlying QTLs have been identified and functionally characterized for phosphorous efficiency, flowering and maturity, pod dehiscence, hard-seededness, α-Tocopherol content, soybean cyst nematode, sudden death syndrome, and salt tolerance. Candidate genes have also been identified for many other quantitative traits for which functional validation is required. Using the sequence information of identified genes from soybean, comparative genomic analysis of homologs in other legume crops could discover novel structural variants and useful alleles for functional marker development. The functional markers may be very useful for molecular breeding in soybean and harnessing benefit of translational research from soybean to other leguminous crops. Thus, soybean crop can act as a model crop for translational genomics and breeding of quantitative traits in legume crops. In this review, we summarize current status of identification and characterization of genes underlying QTLs for various quantitative traits in soybean and their significance in translational genomics and breeding of other legume crops.

A class II KNOX gene, KNOX4, controls seed physical dormancy

Physical dormancy of seed is an adaptive trait that widely exists in higher plants. This kind of dormancy is caused by a water-impermeable layer that blocks water and oxygen from the surrounding environment and keeps embryos in a viable status for a long time. Most of the work on hardseededness has focused on morphological structure and phenolic content of seed coat. The molecular mechanism underlying physical dormancy remains largely elusive. By screening a large number of Tnt1 retrotransposon-tagged Medicago truncatula lines, we identified nondormant seed mutants from this model legume species. Unlike wild-type hard seeds exhibiting physical dormancy, the mature mutant seeds imbibed water quickly and germinated easily, without the need for scarification. Microscopic observations of cross sections showed that the mutant phenotype was caused by a dysfunctional palisade cuticle layer in the seed coat. Chemical analysis found differences in lipid monomer composition between the wild-type and mutant seed coats. Genetic and molecular analyses revealed that a class II KNOTTED-like homeobox (KNOXII) gene, KNOX4, was responsible for the loss of physical dormancy in the seeds of the mutants. Microarray and chromatin immunoprecipitation analyses identified CYP86A, a gene associated with cutin biosynthesis, as one of the downstream target genes of KNOX4 This study elucidated a novel molecular mechanism of physical dormancy and revealed a new role of class II KNOX genes. Furthermore, KNOX4-like genes exist widely in seed plants but are lacking in nonseed species, indicating that KNOX4 may have diverged from the other KNOXII genes during the evolution of seed plants.

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.

A Single-Nucleotide Polymorphism in an Endo-1,4-β-Glucanase Gene Controls Seed Coat Permeability in Soybean

Physical dormancy, a structural feature of the seed coat known as hard seededness, is an important characteristic for adaptation of plants against unstable and unpredictable environments. To dissect the molecular basis of qHS1, a quantitative trait locus for hard seededness in soybean (Glycine max (L) Merr.), we developed a near-isogenic line (NIL) of a permeable (soft-seeded) cultivar, Tachinagaha, containing a hard-seed allele from wild soybean (G. soja) introduced by successive backcrossings. The hard-seed allele made the seed coat of Tachinagaha more rigid by increasing the amount of β-1,4-glucans in the outer layer of palisade cells of the seed coat on the dorsal side of seeds, known to be a point of entrance of water. Fine-mapping and subsequent expression and sequencing analyses revealed that qHS1 encodes an endo-1,4-β-glucanase. A single-nucleotide polymorphism (SNP) introduced an amino acid substitution in a substrate-binding cleft of the enzyme, possibly reducing or eliminating its affinity for substrates in permeable cultivars. Introduction of the genomic region of qHS1 from the impermeable (hard-seeded) NIL into the permeable cultivar Kariyutaka resulted in accumulation of β-1,4-glucan in the outer layer of palisade cells and production of hard seeds. The SNP allele found in the NIL was further associated with the occurrence of hard seeds in soybean cultivars of various origins. The findings of this and previous studies may indicate that qHS1 is involved in the accumulation of β-1,4-glucan derivatives such as xyloglucan and/or β-(1,3)(1,4)-glucan that reinforce the impermeability of seed coats in soybean.

Identification of quantitative trait loci associated with boiled seed hardness in soybean

Boiled seed hardness is an important factor in the processing of soybean food products such as nimame and natto. Little information is available on the genetic basis for boiled seed hardness, despite the wide variation in this trait. DNA markers linked to the gene controlling this trait should be useful in soybean breeding programs because of the difficulty of its evaluation. In this report, quantitative trait locus (QTL) analysis was performed to reveal the genetic factors associated with boiled seed hardness using a recombinant inbred line population developed from a cross between two Japanese cultivars, 'Natto-shoryu' and 'Hyoukei-kuro 3', which differ largely in boiled seed hardness, which in 'Natto-shoryu' is about twice that of 'Hyoukei-kuro 3'. Two significantly stable QTLs, qHbs3-1 and qHbs6-1, were identified on chromosomes 3 and 6, for which the 'Hyoukei-kuro 3' alleles contribute to decrease boiled seed hardness for both QTLs. qHbs3-1 also showed significant effects in progeny of a residual heterozygous line and in a different segregating population. Given its substantial effect on boiled seed hardness, SSR markers closely linked to qHbs3-1, such as BARCSOYSSR_03_0165 and BARCSOYSSR_03_0185, could be useful for marker-assisted selection in soybean breeding.

Identification of a single gene for seed coat impermeability in soybean PI 594619

KEY MESSAGE

Inheritance studies and molecular mapping identified a single dominant gene that conditions seed coat impermeability in soybean PI 594619. High temperatures during seed fill increase the occurrence of soybeans with impermeable seed coat, which is associated with non-uniform and delayed germination and emergence. This can be an issue in soybean production areas with excessively high-temperature environments. The objectives of the present study were to investigate the inheritance of impermeable seed coat under a high-temperature environment in the midsouthern United States and to map the gene(s) that affect this trait in a germplasm line with impermeable seed coat (PI 594619). Crosses were made between PI 594619 and an accession with permeable seed coat at Stoneville, MS in 2008. The parental lines and the segregating populations from reciprocal crosses were grown in Stoneville in 2009. Ninety-nine F2:3 families and parents were also grown at Stoneville, MS in 2011. Seeds were assayed for percent impermeable seed coat using the standard germination test. Genetic analysis of the F2 populations and F2:3 families indicated that seed coat impermeability in PI 594619 is controlled by a single major gene, with impermeable seed coat being dominant to permeable seed coat. Molecular mapping positioned this gene on CHR 2 between markers Sat_202 and Satt459. The designation of Isc (impermeable seed coat) for this single gene has been approved by the Soybean Genetics Committee. Selection of the recessive form (isc) may be important in developing cultivars with permeable seed coat for high-heat production environments. The single-gene nature of impermeable seed coat may also have potential for being utilized in reducing seed damage caused by weathering and mold.

QTL affecting fitness of hybrids between wild and cultivated soybeans in experimental fields

The objective of this study was to identify quantitative trait loci (QTL) affecting fitness of hybrids between wild soybean (Glycine soja) and cultivated soybean (Glycine max). Seed dormancy and seed number, both of which are important for fitness, were evaluated by testing artificial hybrids of G. soja × G. max in a multiple-site field trial. Generally, the fitness of the F₁ hybrids and hybrid derivatives from self-pollination was lower than that of G. soja due to loss of seed dormancy, whereas the fitness of hybrid derivatives with higher proportions of G. soja genetic background was comparable with that of G. soja. These differences were genetically dissected into QTL for each population. Three QTLs for seed dormancy and one QTL for total seed number were detected in the F₂ progenies of two diverse cross combinations. At those four QTLs, the G. max alleles reduced seed number and severely reduced seed survival during the winter, suggesting that major genes acquired during soybean adaptation to cultivation have a selective disadvantage in natural habitats. In progenies with a higher proportion of G. soja genetic background, the genetic effects of the G. max alleles were not expressed as phenotypes because the G. soja alleles were dominant over the G. max alleles. Considering the highly inbreeding nature of these species, most hybrid derivatives would disappear quickly in early self-pollinating generations in natural habitats because of the low fitness of plants carrying G. max alleles.

A model to predict the frequency of integration of fitness-related QTLs from cultivated to wild soybean

With the proliferation of genetically modified (GM) products and the almost exponential growth of land use for GM crops, there is a growing need to develop quantitative approaches to estimating the risk of escape of transgenes into wild populations of crop relatives by natural hybridization. We assessed the risk of transgene escape by constructing a population genetic model based on information on fitness-related QTLs obtained from an F (2) population of wild soybean G. soja × cultivated soybean Glycine max. Simulation started with ten F (1) and 990 wild soybeans reproducing by selfing or outcrossing. Seed production was determined from the genetic effects of two QTLs for number of seeds (SN). Each seed survived winter according to the maternal genotype at three QTLs for winter survival (WS). We assumed that one neutral transgene was inserted at various sites and calculated its extinction rate. The presence of G. max alleles at SN and WS QTLs significantly decreased the probability of introgression of the neutral transgene at all insertion sites equally. The presence of G. max alleles at WS QTLs lowered the risk more than their presence at SN QTLs. Although most model studies have concentrated only on genotypic effects of transgenes, we show that the presence of fitness-related domestication genes has a large effect on the risk of transgene escape. Our model offers the advantage of considering the effects of both domestication genes and a transgene, and they can be widely applied to other wild × crop relative complexes.

The origin and fate of morphological intermediates between wild and cultivated soybeans in their natural habitats in Japan

The spread of transgenes into the genome of wild soybean is a concern when transgenic and wild soybeans are planted sympatrically. The objectives of this study were to investigate the origin and fate of morphological intermediates between wild and cultivated soybeans in their natural habitats in Japan. Twenty nuclear microsatellite and two chloroplast dCAPS markers were used to evaluate genetic variation of 468 wild, 17 intermediate, and 12 cultivated soybean samples collected from six sites between 2003 and 2006. Allelic differentiation of microsatellite markers between wild and cultivated soybeans was sufficient to detect their hybrids. Based on levels of observed heterozygosity, intermediate soybean plants were from two generations: either F(1) or an early segregating generation. Genetic admixture analysis and parentage assignment analysis revealed that the parents of all intermediate soybean plants could be assigned to a particular wild soybean plant and late-maturing cultivar. The chloroplast DNA haplotypes revealed that all intermediate soybean plants originated from gene flow from cultivated to wild soybeans at all sites. Based on monitoring at both the phenotypic and molecular levels, hybrids quickly disappeared from natural habitats, and secondary gene flow from these plants to wild soybean was not detected. Thus, while gene flow from transgenic soybean into wild soybean can occur, gene introgression appears to be rare in natural habitats in Japan. This is the first report on the detection of gene flow from cultivated to wild soybean at the molecular level.

Properties of the soybean seed coat cuticle change during development

Whether a seed coat of a soybean (Glycine max L. Mer.) seed is permeable or non-permeable is governed by a number of quantitative trait loci further influenced by environmental factors. In soybean seeds, water loss is controlled by a thin, inconspicuous outer cuticle. When intact, the outer cuticle constitutes a barrier to water passage; however, the presence of minute cracks in the cuticle results in the ready passage of water. We explored the timing of cuticular development in soybean seeds by measuring the deposition of the cutin in relation to seed growth and cell viability. Cutin deposition occurred early in the development and ceased just prior to the final stage of rapid seed expansion. Cracks in the cuticle appeared after cutin synthesis ceased while the seed continued to grow. In permeable seeds (regardless of genotype) the resistance of the cuticle to water passage increased steadily during development until seed expansion was maximal and cracks appeared in the cuticle. Once cracks formed, they became the primary site of water passage and the cuticle lost its ability to control the process. In non-permeable seeds, no cracks appeared at this critical point and the cuticle continued to restrict water passage. Microarray analysis of gene expression during seed coat development revealed a complex transcriptome with many genes uniquely expressed in the seed coat. However, the expression patterns were remarkably similar between permeable and non-permeable types, in keeping with the complexity of the underlying genetics of seed coat permeability.

Putative quantitative trait loci associated with calcium content in soybean seed

Seed calcium content is an important quality attribute of specialty soybean [Glycine max (L.) Merr.] for soyfoods. However, analyzing seed for calcium content is time consuming and labor intensive. Knowing quantitative trait loci (QTL) for seed calcium will facilitate the development of elite cultivars with proper calcium content through marker-assisted selection (MAS). The objective of this study was to identify major QTL associated with calcium content in soybean seed. Calcium content was tested in 178 F(2:3) and 157 F(2:4) lines derived from the cross of SS-516 (low calcium) x Camp (high calcium). The F(2:3) lines were genotyped with 148 simple sequence repeat markers in a previous study on seed hardness, and the genotypic data were used in the QTL analysis of the current study. Four QTL designated as Ca1, Ca2, Ca3, and Ca4 on linkage groups (LGs) A2, I, and M were identified by both single-marker analysis and composite-interval mapping, and the QTL accounted for 10.7%, 16.3%, 14.9%, and 9.7% of calcium content variation, respectively. In addition, multiple-interval mapping analysis revealed a significant dominant-by-dominant interaction effect between Ca1 and Ca3, which accounted for 4.3% calcium content variation. These QTL will facilitate the implementation of MAS for calcium content in soybean-breeding programs.

Identification of SSR markers associated with seed coat permeability and electrolyte leaching in soybean

Seed coat permeability and electrolyte leaching are the important traits that have been negatively associated with seed longevity in soybean. The objective of this study was to use SSR markers to identify genomic regions significantly associated with QTLs controlling seed coat permeability and electrolyte leaching in a segregating F2 population derived from a cross of Birsa soya-1 x JS 71-05. Parental polymorphism survey using 145 SSR markers identified 21 polymorphic ones, which were used to genotype 153 F2 individuals. Four independent markers (Satt434, Satt538, Satt281 and Satt598) were significantly (P=0.05) associated with seed coat permeability. One of these markers (Satt 281) also showed significant association with electrolyte leaching that partly supported the observed positive correlation (r = 0.425) between the two traits. Markers for seed coat permeability individually explained 3.9% to 4.5% of the total phenotypic variation, while the marker linked with electrolyte leaching explained 5.6% of the total variation.

The genetics of domestication of the azuki bean (Vigna angularis)

Genetic differences between azuki bean (Vigna angularis var. angularis) and its presumed wild ancestor (V. angularis var. nipponensis) were resolved into QTL for traits associated with adaptation to their respective distinct habits. A genetic linkage map constructed using progenies from a cross between Japanese cultivated and wild azuki beans covers 92.8% of the standard azuki bean linkage map. A reciprocal translocation between cultivated and wild azuki bean parents was identified on the basis of the linkage map having a pseudolinkage group and clustering of seed productivity-related QTL with large effect near the presumed breakpoints. In total, 162 QTL were identified for 46 domestication-related traits. Domestication of azuki bean has involved a trade-off between seed number and seed size: fewer but longer pods and fewer but larger seeds on plants with shorter stature in cultivated azuki bean being at the expense of overall seed yield. Genes found related to germination and flowering time in cultivated azuki bean may confer a selective advantage to the hybrid derivatives under some ecological conditions and may explain why azuki bean has evolved as a crop complex in Japan.

An updated 'Essex' by 'Forrest' linkage map and first composite interval map of QTL underlying six soybean traits

DNA marker maps based on single populations are the basis for gene, loci and genomic analyses. Individual maps can be integrated to produce composite maps with higher marker densities if shared marker orders are consistent. However, estimates of marker order in composite maps must include sets of markers that were not polymorphic in multiple populations. Often some of the pooled markers were not codominant, or were not correctly scored. The soybean composite map was composed of data from five separate populations based on northern US germplasm but does not yet include 'Essex' by 'Forrest' recombinant inbred line (RIL) population (E x F) or any southern US soybean cultivars. The objectives were, to update the E x F map with codominant markers, to compare marker orders among this map, the Forrest physical map and the composite soybean map and to compare QTL identified by composite interval maps to the earlier interval maps. Two hundred and thirty seven markers were used to construct the core of the E x F map. The majority of marker orders were consistent between the maps. However, 19 putative marker inversions were detected on 12 of 20 linkage groups (LG). Eleven marker distance compressions were also found. The number of inverted markers ranged from 1 to 2 per LG. Thus, marker order inversions may be common in southern compared to northern US germplasm. A total of 61 QTL among 37 measures of six traits were detected by composite interval maps, interval maps and single point analysis. Seventeen of the QTL found in composite intervals had previously been detected among the 29 QTL found in simple interval maps. The genomic locations of the known QTL were more closely delimited. A genome sequencing project to compare Southern and Northern US soybean cultivars would catalog and delimit inverted regions and the associated QTL. Gene introgression in cultivar development programs would be accelerated.

Segregation distortion for seed testa color in Mungbean (Vigna radiata L. Wilcek)

Genetic segregation experiments with plant species are commonly used for understanding the inheritance of traits. A basic assumption in these experiments is that each gamete developed from megasporogenesis has an equal chance of fusing with a gamete developed from microsporogenesis, and every zygote formed has an equal chance of survival. If gametic and/or zygotic selection occurs whereby certain gametes or zygotic combinations have a reduced chance of survival, progeny distributions are skewed and are said to exhibit segregation distortion. In this study, inheritance data are presented for the trait seed testa color segregating in large populations (more than 200 individuals) derived from closely related mungbean (Vigna radiata L. Wilcek) taxa. Segregation ratios suggested complex inheritance, including dominant and recessive epistasis. However, this genetic model was rejected in favor of a single-gene model based on evidence of segregation distortion provided by molecular marker data. The segregation distortion occurred after each generation of self-pollination from F1 thru F7 resulting in F7 phenotypic frequencies of 151:56 instead of the expected 103.5:103.5. This study highlights the value of molecular markers for understanding the inheritance of a simply inherited trait influenced by segregation distortion.

Identification of putative QTL that underlie yield in interspecific soybean backcross populations

Glycine soja, the wild progenitor of soybean, is a potential source of useful genetic variation in soybean improvement. The objective of our study was to map quantitative trait loci (QTL) from G. soja that could improve the crop. Five populations of BC(2)F(4)-derived lines were developed using the Glycine max cultivar IA2008 as a recurrent parent and the G. soja plant introduction (PI) 468916 as a donor parent. There were between 57 and 112 BC(2)F(4)-derived lines in each population and a total of 468 lines for the five populations. The lines were evaluated with simple sequence repeat markers and in field tests for yield, maturity, plant height, and lodging. The field testing was done over 2 years and at two locations each year. Marker data were analyzed for linkage and combined with field data to identify QTL. Using an experimentwise significance threshold of P=0.05, four yield QTL were identified across environments on linkage groups C2, E, K, and M. For these yield QTL, the IA2008 marker allele was associated with significantly greater yield than the marker allele from G. soja. In addition, one lodging QTL, four maturity QTL, and five QTL for plant height were identified across environments. Of the 14 QTL identified, eight mapped to regions where QTL with similar effects were previously mapped. Many regions carrying the yield QTL were also significant for other traits, such as plant height and lodging. When the significance threshold was reduced and the data were analyzed with simple linear regression, four QTL with a positive allele for yield from G. soja were mapped. One epistatic interaction between two genetic regions was identified for yield using an experimentwise significance threshold of P=0.05. Additional research is needed to establish whether multiple trait associations are the result of pleiotropy or genetic linkage and to retest QTL with a positive effect from G. soja.

FISH mapping of the 5S and 18S-28S rDNA loci in different species of Glycine

Wild germplasms are often the only significant sources of useful traits for crops, such as soybean, that have limited genetic variability. Before these germplasms can be effectively manipulated they must be characterized at the cytological and molecular levels. Modern soybean probably arose through an ancient allotetraploid event and subsequent diploidization of the genome. However, wild Glycine species have not been intensively investigated for this ancient polyploidy. In this article we determined the number of both the 5S and 18S-28S rDNA sequences in various members of the genus Glycine using FISH. Our results distinctly establish the loss of a 5S rDNA locus from the "diploid" (2n = 40) species and the loss of two from the (2n = 80) polyploids of GLYCINE: A similar diploidization of the 18S-28S rDNA gene family has occurred in G. canescens, G. clandestina, G. soja, and G. max (L.) Merr. (2n = 40). Although of different genome types, G. tabacina and G. tomentella (2n = 80) both showed two major 18S-28S rDNA loci per haploid genome, in contrast to the four loci that would be expected in chromosomes that have undergone two doubling events in their evolutionary history. It is evident that the evolution of the subgenus Glycine is more complex than that represented in a simple diploid-doubled to tetraploid model.

RFLP loci associated with soybean seed protein and oil content across populations and locations

Molecular markers provide the opportunity to identify marker-quantitative trait locus (QTL) associations in different environments and populations. Two soybean [Glycine max (L.) Merr.] populations, 'Young' x PI 416 937 and PI 97100 x 'Coker 237', were evaluated with restriction fragment length polymorphism (RFLP) markers to identify additional QTLs related to seed protein and oil. For the Young x PI 416937 population, 120 F4-derived lines were secored for segregation at 155 RFLP loci. The F4-derived lines and two parents were grown at Plains, G.a., and Windblow and Plymouth, N.C. in 1994, and evaluated for seed protein and oil. For the PI 97100 x Coker 237 population, 111 F2-derived lines were evaluated for segregation at 153 RFLP loci. Phenotypic data for seed protein and oil were obtained in two different locations (Athens, G.a., and Blackville, S.C.) in 1994. Based on single-factor analysis of variance (ANOVA) for the Young x PI 416937 population, five of seven independent markers associated with seed protein, and all four independent markers associated with seed oil in the combined analysis over locations were detected at all three locations. For the PI 97 100 x Coker 237 population, both single-factor ANOVA and interval mapping were used to detect QTLs. Using single-factor ANOVA, three of four independent markers for seed protein and two of three independent markers for seed oil were detected at both locations. In both populations, singlefactor ANOVA, revealed the consistency of QTLs across locations, which might be due to the high heritability and the relatively few QTLs with large effects conditioning these traits. However, interval mapping of the PI 97100 x Coker 237 population indicated that QTLs identified at Athens for seed protein and oil were different from those at Blackville. This might result from the power of QTL mapping being dependent on the level of saturation of the genetic map. Increased seed protein was associated with decreased seed oil in the PI 97100 x Coker 237 population (r = -0.61). There were various common markers (P[Symbol: see text]0.05) on linkage groups (LG) E, G,H,K, and UNK2 identified for both seed protein and oil. One QTL on LG E was associated with seed protein in both populations. The other QTLs for protein and oil were population specific.

Molecular-marker analysis of seed-weight: genomic locations, gene action, and evidence for orthologous evolution among three legume species

The objectives of this study were to use molecular markers to: (1) identify quantitative trait loci (QTL) controlling seed-weight in soybean, (2) characterize the genetic basis of seed-weight expression, and (3) determine whether soybean shares orthologous seed-weight genes with cowpea and/or mung bean. An F2 population was developed between a large-seeded Glycine max breeding line and a small-seeded G. soja plant introduction. DNA samples from 150 F2 individuals were analyzed with 91 polymorphic genetic markers, including RFLPs, RAPDs and SSRs. Seed-weight was analyzed by randomly sampling 100 seeds from each of 150 greenhouse-grown F2 individuals, and their 150 F2∶3 lines, from a replicated field trial. Markers associated with seed-weight were identified using the computer program MapMaker-QTL and a one-way analysis of variance. Three and five markers were significantly associated with seed-weight variation (P<0.01) in the F2 and F2∶3 generations, respectively. Tests for digenic epistasis revealed three significant interactions in both generations. In a combined analysis, these markers and interactions explained 50 and 60% of the phenotypic variation for seed-weight in the F2 and F2∶3 generations, respectively. Comparison of our results in soybean (Glycine) with those previously reported in cowpea and mung bean (Vigna) indicated that soybean and cowpea share an orthologous seed-weight gene. In both species, a genomic region significantly associated with seed-weight spanned the same RFLP markers in the same linkage order. A significant digenic interaction involving this genomic region was conserved in all three species. These results suggest that the exploitation of "comparative QTL mapping" is an invaluable tool for quantitative geneticists working with poorly characterized plant systems.

Quantitative trait analysis of fruit quality in cucumber: QTL detection, confirmation, and comparison with mating-design variation

A cross within C. sativus var. sativus (GY14 x P1432860) and molecular markers were used to determine the number, magnitudes of effect, and overall variation described for genes conditioning the quantitatively inherited traits of length, diameter, seed-cavity size, color, L/D (length/diameter), and S/D (seed-cavity size/diameter). QTL effects were detected with MAPMAKER/QTL using 100 F3 lines evaluated in a replicated field trial of two harvests over 2 years at one location. Multilocus models were constructed by fixing significant intervals and re-scanning using MAPMAKER/ QTL. Marker inclusion in multilocus models was compared to an ANOVA "backward elimination" procedure. Generally the same loci were associated with QTLs among the two methods of model construction. Heritabilities of individual QTLs were confirmed by analysis of related backcrosses (67 BC1P1 lines and 68 BC1 P2 lines). The majority of QTLs were confirmed in at least one backcross population. Pairs of backcrosses allowed overall additive variances and heritabilities to be calculated using a North Carolina Design III (NCIII design) and estimates were compared to overall variances attributable to markers. Heritability estimates using markers were comparable, but generally lower than additive variances estimated by co-variance relationships in the NCIII design. This suggests that neither the number nor the magnitude of QTL effects were overestimated. The utility of backcrosses to confirm individual QTLs and the overall variance described by QTLs is recommended to avoid false positives and over-estimation of effects. The number of QTLs, and/or the proportions of phenotypic variation described by markers and the mating design, agreed with previous reports of heritabilities employing similar germplasm.

A single nuclear locus phylogeny of soybean based on DNA sequence

Soybean [Glycine max (L.) Merr.] evolution was examined by sequencing portions of the restriction fragment length polymorphism (RFLP) locus A-199a of 21 taxa from the Glycininae and 1 from the Phaseoleae. Four hundred nucleotides were determined in each, aligned, and then compared for these taxa. Within the annual soybean subgenus (Soja), the four accessions differed at as many as 2.2% of the nucleotides. Among 13 perennial soybean species (subgenus Glycine), nucleotide variation ranged from 1.7% to 8.4%. The nucleotide difference between the two soybean subgenera was 3.0-7.0%. Nucleotide variation between the genus Glycine and the related genera of Neonotonia, Amphicarpa, Teramnus, and Phaseolus ranged from 8.2% to 16.4%. In addition to nucleotide substitutions, insertions/deletions (indels) differences were also observed and were consistent with nucleotide-based analysis. Cladistic analysis of the A-199a sequences was performed using Wagner parsimony to construct a soybean phylogeny. Sixteen equally parsimonious trees were produced from these data. The trees were 246 steps in length with a consistency index of 0.78. Indels distribution upon the consensus topology revealed a pattern congruent with the nucleotide-based phylogeny. The current taxonomic status of the soybean subgenera and the related genera of Neonotonia, Amphicarpa, and Teramnus were well-supported and appear monophyletic in this analysis. Homoplasy within the subgenus Glycine led to a lack of resolved topology for many of these 13 taxa. However, the Glycine clade topology was consistent with phylogenies proposed using crossing experiments and cpDNA RFLPs. These genera were arranged from ancestral to derived as: Teramnus, Amphicarpa, Neonotonia, and Glycine when Phaseolus vulgaris was used as an outgroup.

Molecular marker analysis of genes controlling morphological variation in Brassica rapa (syn. campestris)

Construction of a detailed RFLP linkage map of B. rapa (syn. campestris) made it possible, for the first time, to study individual genes controlling quantitative traits in this species. Ninety-five F2 individuals from a cross of Chinese cabbage cv 'Michihili' by Spring broccoli were analyzed for segregation at 220 RFLP loci and for variation in leaf, stem, and flowering characteristics. The number, location, and magnitude of genes underlying 28 traits were determined by using an interval mapping method. Zero to five putative quantitative trait loci (QTL) were detected for each of the traits examined. There were unequal gene effects on the expression of many traits, and the inheritance patterns of traits ranged from those controlled by a single major gene plus minor genes to those controlled by polygenes with small and similar effects. The effect of marker locus density on detection of QTL was analyzed, and the results showed that the number of QTL detected did not change when the number of marker loci used for QTL mapping was decreased from 220 to 126; however, a further reduction from 126 to 56 caused more than 15% loss of the total QTL detected. The detection of putative minor QTL by removing the masking effects of major QTL was explored.

A RFLP linkage map of Sorghum bicolor (L.) Moench

A RFLP linkage map of sorghum composed principally of markers detected with sorghum low-copy-number nuclear DNA clones has been constructed. The map spans 1789 cMs and consists of 190 loci grouped into 14 linkage groups. The 10 largest linkage groups consist of from 10 to 24 markers and from 103 to 237 cMs, and the other 4 linkage groups consist of from 2 to 5 markers and from 7 to 62 cMs. The map was derived in Sorghum bicolor ssp. bicolor by analysis of a F2 population composed of 50 plants derived from a cross of IS 3620C, a guinea line, and BTx 623, an agronomically important inbred line derived from a cross between a zera zera (a caudatum-like sorghum) and an established kafir line. The restriction fragment length polymorphism (RFLP) frequency detected in this population using polymerase chain reaction (PCR)-amplifiable low-copy-number sorghum clones and five restriction enzymes was 51%. A minimal estimate of the number of clones that detect duplicate sequences is 11 %. Null alleles occurred at 13% of the mapped RFLP loci.

Quantitative trait locus analysis of tuber dormancy in diploid potato (Solanum spp.)

Quantitative trait locus (QTL) analysis for tuber dormancy was performed in a diploid potato population (TRP133) consisting of 110 individuals. The female parent was a hybrid between haploid S. tuberosum (2x) and S. chacoense, while the male parent was a S. phureja clone. The population was characterized for ten isozyme loci, 44 restriction fragment length polymorphisms (RFLPs) and 63 random amplified polymorphic DNAs (RAPDs). Eighty-seven of these loci segregating from the female parent were utilized to develop a linkage map that comprised 10 of the 12 chromosomes in the genome. Dormancy, as measured by days-to-sprouting after harvest, ranged from 10 to 90 days, with a mean of 19 days. QTLs were mapped by conducting one-way analyses of variance for each marker locus by dormancy combination. Twenty-two markers had a significant association with dormancy, identifying six putative QTLs localized on each of chromosomes 2, 3, 4, 5, 7 and 8. The QTL with the strongest effect on dormancy was detected on chromosome 7. A multilocus model was developed using the locus with highest R(2) value in each QTL. This model explained 57.5% of the phenotypic variation for dormancy. Seven percent of possible epistatic interactions among significant markers were significant when tested through two-way analyses of variance. When these were included in the main-effects model, it explained 72.1% of the phenotypic variation for dormancy. QTL analysis in potato, the methodology to transfer traits and interactions into the 4x level, and QTLs of value for marker-assisted selection, are discussed.

Mapping oligogenic resistance to powdery mildew in mungbean with RFLPs

We have used restriction fragment length polymorphisms (RFLPs) to map genes in mungbean (Vigna radiata) that confer partial resistance to the powdery mildew fungus, Erysiphe polygoni. DNA genotypes for 145 RFLP loci spanning 1570 centimorgans of the mungbean genome were assayed in a population of 58 F2 plants. This population was derived from a cross between a moderately powdery mildew resistant ("VC3980A") and a susceptible ("TC1966") mungbean parent. F3 lines derived from the F2 plants were assayed in the field for powdery mildew response and the results were compared to the RFLP genotype data, thereby identifying loci associated with powdery mildew response. A total of three genomic regions were found to have an effect on powdery mildew response, together explaining 58% of the total variation. At 65 days after planting, two genomic regions were significantly associated with powdery mildew resistance. For both loci, the allele from "VC3890A" was associated with increased resistance. At 85 days, a third genomic region was also associated with powdery mildew response. For this locus, the allele from the susceptible parent ("TC1966") was the one associated with higher levels of powdery mildew resistance. These results indicate that putative partial resistance loci for powdery mildew in mungbean can be identified with DNA markers, even in a population of modest size analyzed at a single location in a single year.

Quantitative trait loci influencing protein and starch concentration in the Illinois Long Term Selection maize strains

A study was initiated to determine the number, chromosomal location, and magnitude of effect of QTL (quantitative trait loci or locus depending on context) controlling protein and starch concentration in the maize (Zea mays L.) kernel. Restriction fragment length polymorphism (RFLP) analysis was performed on 100 F3 families derived from a cross of two strains, Illinois High Protein (IHP), X Illinois Low Protein (ILP), which had been divergently selected for protein concentration for 76 generations as part of the Illinois Long Term Selection Experiment. These families were analyzed for kernel protein and starch in replicated field trials during 1990 and 1991. A series of 90 genomic and cDNA clones distributed throughout the maize genome were chosen for their ability to detect RFLP between IHP and ILP. These clones were hybridized with DNA extracted from the 100 F3 families, revealing 100 polymorphic loci. Single factor analysis of variance revealed significant QTL associations of many loci with both protein and starch concentration (P < 0.05 level). Twenty-two loci distributed on 10 chromosome arms were significantly associated with protein concentration, 19 loci on 9 chromosome arms were significantly associated with starch concentration. Sixteen of these loci were significant for both protein and starch concentration. Clusters of 3 or more significant loci were detected on chromosome arms 3L, 5S, and 7L for protein concentration, suggesting the presence of QTL with large effects at these locations. A QTL with large additive effects on protein and starch concentration was detected on chromosome arm 3L. RFLP alleles at this QTL were found to be linked with RFLP alleles at the Shrunken-2 (Sh2) locus, a structural gene encoding the major subunit of the starch synthetic enzyme ADP-glucose pyrophosphorylase. A multiple linear regression model consisting of 6 significant RFLP loci on different chromosomes explained over 64 % of the total variation for kernel protein concentration. Similar results were detected for starch concentration. Thus, several chromosomal regions with large effects may be responsible for a significant portion of the changes in kernel protein and starch concentration in the Illinois Long Term Selection Experiment.

Evaluation of soybean RFLP marker diversity in adapted germ plasm

Soybean RFLP markers have been primarily developed and genetically mapped using wide crosses between exotic and adapted genotypes. We have screened 38 soybean lines at 128 RFLP marker loci primarily to characterize germ plasm structure but also to evaluate the utility of RFLP markers identified in unadapted populations. Of these DNA probes 70% detected RFLPs in this set of soybean lines with an average polymorphism index of 0.30. This means that only 1 out of 5 marker loci was informative between any particular pair of adapted soybean lines. The variance associated with the estimation of RFLP genetic distance (GDR) was determined, and the value obtained suggested that the use of more than 65-90 marker loci for germ plasm surveys will add little precision. Cluster analysis and principal coordinate analysis of the GDR matrix revealed the relative lack of diversity in adapted germ plasm. Within the cultivated lines, several lines adapted to Southern US maturity zones also appeared as a separate group. GDR data was compared to the genetic distance estimates obtained from pedigree analysis (GDP). These two measures were correlated with r = 0.54 for all 38 lines, but the correlation increased to r = 0.73 when only adapted lines were analyzed.

A genetic map of citrus based on the segregation of isozymes and RFLPs in an intergeneric cross

Isozymes and restriction fragment length polymorphisms were used as markers in the construction of a genetic map of the citrus nuclear genome. The map was based on the segregation of 8 isozyme, 1 protein, and 37 RFLP loci in 60 progeny of a cross of two intergeneric hybrids, 'Sacaton' citrumelo (Citrus paradisi Macf. x Poncirus trifoliata (L.) Raf.) and 'Troyer' citrange (C. sinensis (L.) Osbeck x P. trifoliata), often used as rootstocks. The map contains 38 of 46 studied loci distributed on ten linkage groups. A genome size of 1,700 cM was estimated from partial linkage data. Approximately 35% of the genome should be within 10 cM and 58% within 20 cM of the mapped markers. Eight loci in three linkage groups and 1 unlinked locus deviated significantly from Mendelian segregation.

RFLP analysis of soybean seed protein and oil content

The objectives of this study were to present an expanded soybean RFLP map and to identify quantitative trait loci (QTL) in soybean [Glycine max (L.) Merr.] for seed protein and oil content. The study population was formed from a cross between a G. max experimental line (A81-356022) and a G. soja Sieb. and Zucc. plant introduction (PI 468916). A total of 252 markers was mapped in the population, forming 31 linkage groups. Protein and oil content were measured on seed harvested from a replicated trial of 60 F2-derived lines in the F3 generation (F2∶3 lines). Each F2∶3 line was genotyped with 243 RFLP, five isozyme, one storage protein, and three morphological markers. Significant (P<0.01) associations were found between the segregation of markers and seed protein and oil content. Segregation of individual markers explained up to 43% of the total variation for specific traits. All G. max alleles at significant loci for oil content were associated with greater oil content than G. soja alleles. All G. soja alleles at significant loci for protein content were associated with greater protein content than G. max alleles.

Restriction fragment length polymorphism and allozyme linkage map of Cuphea lanceolata

Cuphea lanceolata Ait. has had a significant role in the domestication of Cuphea and is a useful experimental organism for investigating how medium-chain lipids are synthesized in developing seeds. To expand the genetics of this species, a linkage map of the C. lanceolata genome was constructed using five allozyme and 32 restriction-fragment-length-polymorphism (RFLP) marker loci. These loci were assigned to six linkage groups that correspond to the six chromosomes of this species. Map length is 288 cM. Levels of polymorphism were estimated for three inbred lines of C. lanceolata and an inbred line of C. viscosissima using 84 random genomic clones and two restriction enzymes, EcoRI and HindIII. Of the probes 29% detected RFLPs between C. lanceolata and C. viscosissima lines. Crosses between these species can be exploited to expand the map.

Plant genome studies: restriction fragment length polymorphism and chromosome mapping information

The detection of sequence variation with restriction fragment length polymorphisms is advancing our knowledge of plant genetics on several fronts. In the past year, there has been progress in genetic map construction, phylogeny studies, and the dissection of multigenic traits. In addition, new methods that are independent of restriction sites are being developed for polymorphism detection.

Analyses of Phaseolus vulgaris L. and P. coccineus Lam. hybrids by RFLP: preferential transmission of P. vulgaris alleles

Restriction fragment length polymorphism (RFLP) was determined among P. vulgaris genotypes and Phaseolus species using 19 probes. The incidence of polymorphism was high (70-86%) between species, but relatively low (22-26%) between genotypes of P. vulgaris. Suitable probes were identified for the analysis of P. vulgaris and P. coccineus hybrids. The segregation pattern in F2 populations was Mendelian for two probes (LHB and VEE20) and non-Mendelian for GS-g, CHS, and CHI. Statistical analyses indicated gametic selection with preferential transmission of the P. vulgaris alleles, which may account for the selective recovery of P. vulgaris progeny types observed earlier. The available hybrids of P. vulgaris and P. coccineus and the high degree of interspecific RFLP will facilitate the construction of a linkage map for Phaseolus.