Inheritance mode of fruit traits in melon: Heterosis for fruit shape and its correlation with genetic distance

Fruit quality traits were studied in 12 exotic accessions and their hybrids with a “Piel de Sapo” inodorus melon cultivar. The genetic relationships among these genotypes were assessed with 16 microsatellite markers, which agreed with the classification of Cucumis callosus, C. pubescens and C. trigonus as accessions within C. melo. There were very large differences between all the exotic accessions and “Piel de Sapo” genotype for fruit traits. When the hybrids were analysed, three different situations regarding mid parent heterosis were found, depending on the trait: no heterosis (soluble solid concentration), highly variable, from negative to positive (fruit weight and fruit diameter) and general positive heterosis (ovary shape, fruit length and fruit shape). Best parent heterosis for fruit shape was also common among hybrids. A highly significant correlation (r = 0.81) was detected between fruit shape and fruit length heterosis, suggesting that fruit shape heterosis is caused mainly by the enlargement of the fruit longitudinally. A highly significant correlation (r = 0.84) between heterosis for fruit shape and genetic distance, as estimated with microsatellites, was also found. These results, together with the previously reported observation that melon fruit shape is polygenic and highly heritable, makes the genetics of melon fruit shape a suitable system for dissecting the genetic and molecular basis of heterosis.     

Variation in cooking and eating quality traits in Japanese rice germplasm accessions

The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan.     

Variations for Fusarium head blight resistance associated with genomic diversity in different sources of the resistant wheat cultivar ‘Sumai 3’

Fusarium head blight (FHB), caused by Fusarium graminearum, is a serious disease of wheat (Triticum aestivum L.) associated with contamination by the mycotoxin deoxynivalenol (DON). The FHB-resistant wheat cultivar ‘Sumai 3’ has been used extensively around the world. The existence of variation in FHB resistance among ‘Sumai 3’ accessions has been discussed. In this study, genetic variation among ‘Sumai 3’ accessions collected from six countries were identified using SSR markers; our results demonstrate unique chromosome regions in Sumai 3-AUT and Sumai 3-JPN (‘Sumai 3’ accessions from Austria and Japan, respectively). Field evaluation indicated strong resistance to FHB in Sumai 3-AUT. The polymorphic rate (number of polymorphic markers/number of available markers × 100) based on a DArT array was 12.5% between the two ‘Sumai 3’ accessions. Genotyping for DNA markers flanking FHB-resistant quantitative trait loci (QTLs) revealed genetic variations for the QTL regions on 5AS and 2DS; however, no variation was observed for the QTL regions on 3BS and 6B. Thus, the variation in FHB resistance among ‘Sumai 3’ accessions in the field is due to genetic diversity.     

Genetic diversity revealed in the apomictic fruit species Garcinia mangostana L. (mangosteen)

The novel molecular marker technique Randomly Amplified DNA Fingerprinting (RAF)was used to survey genetic relationships between 37 accessions of the tropical fruit G. mangostana (mangosteen) and among 11 accessions from eight other Garcinia species. Although mangosteen is believed to reproduce exclusively through apomixis, our results show that considerable genetic diversity exists within G. mangostana and between other Garcinia species. Among the 37G. mangostana accessions examined, nine different genotypes were identified which clustered into three distinct groups based on correspondence analysis(reciprocal averaging). For 26 (70%) of the accessions no marker variation was detected over 530 loci screened. A further eight (22%) accessions exhibited very low levels of variation (0.2–1%) suggesting at least one well conserved mangosteen genotype. The remaining three accessions (8%) showed extensive variation (22–31%)compared with the majority of accessions. The three mangosteen groups were 63–70% dissimilar to the other Garciniaspecies investigated. The genetic diversity identified in this research will assist in the conservation of Garciniagermplasm and provides a valuable framework for the genetic improvement of mangosteen. This revised version was published online in August 2006 with corrections to the Cover Date.     

Characterization of six varieties of Cucumis melo L. based on morphological and physiological characters, including shelf-life of fruit

Seventy-two accessions covering six varieties of Cucumis melo were characterized by using 35 morphological characters with emphasis on shelf-life, and the relationships between shelf-life and related characters was investigated. Principal component analysis (PCA) revealed that development period of plant and fruit, size of seed and fruit, shelf-life, stem hair, flesh juiciness, netting, abscission of peduncle, rapid yellowing of epidermis at maturity, Brix value, and color of flesh and epidermis etc. were the principal characters to discriminate melon accessions examined in the present study. According to the scatter diagram, vars. acidulusand makuwa, both of which belong to the Oriental melon, are closely related because of their short growth duration, small seed, thin pericarp and poor shelf-life, while American cantaloupe (var.reticulatus) and European cantaloupe (var. cantalupensis) are rather closely related due to their climacteric fruit with orange flesh, slipped peduncle and rapid yellowing of epidermis at maturity, which is closely related with their shelf-life. PCA also indicated that var. saccharinus was closer to var. inodorus than to the other varieties, due to their requirement of long period for development, large size of seed and fruit, and half- or non-slipped peduncle. Shelf-life of melon fruit was significantly correlated with the following characters: quality of flesh, size of seed and fruit, abscission of peduncle, development periods of plant and fruit, rapid yellowing of epidermis at maturity, Brix value and color of flesh and epidermis. Accessions with good shelf-life were mostly found in vars. saccharinus and inodorus. This revised version was published online in July 2006 with corrections to the Cover Date.     

Phenotypic diversity and identification of wild Arachis accessions with useful agronomic and nutritional traits

Wild relatives harbor novel sources of variation, which can be used to enhance the genetic base of a cultivar gene pool. A total of 269 accessions from 20 wild Arachis species belonging to six sections were evaluated for 41 morpho-agronomic traits and 89 selected accessions for oil, protein and total sugar content. Six plants from each accession were grown in an open Arachis house in large-cylindrical concrete structures during the 2004?C2005 season at Patancheru, India. REML analysis showed significant differences between species and accessions for most of the traits studied. Hierarchical cluster analysis, based on the first five principal component scores accounted for 82.5% variation, resulting in four clusters. Variation in genome relationships and ploidy levels had no bearing on the clustering pattern which was predominated by life forms: clusters 1 and 2, contained mostly annuals and clusters 3 and 4 perennials. A large range of variations were noticed among species for some of the agronomic traits: days to flowering, pod and seed characteristics, specific leaf area (SLA) and for SPAD chlorophyll meter reading (SCMR). Arachis duranensis showed the maximum intraspecific variation as revealed by a high diversity index for 23 of the 41 traits which included: days to flowering, primary branches, plant width, pod length, pod width, SCMR and SLA. The other species with desirable traits were A. pusilla (earliest flowering) and A. villosa (high SCMR at 60 and 80 days after sowing). The latter species is cross compatible with cultivated groundnut, thus, is a good source to enhance the trait value in the cultigen??s gene pool. The best 20 accessions with superior agronomic, nutritional quality and drought related trait combinations have been identified for their use in introgression of diverse and unique alleles from wild Arachis species into A. hypogaea.     

Natural variation in photoperiodic flowering pathway and identification of photoperiod-insensitive accessions in wild wheat, <Emphasis Type="Italic">Aegilops tauschii</Emphasis>

The D-genome progenitor of hexaploid wheat, Aegilops tauschii Coss., has a wide natural species range in central Eurasia and possesses wide natural variation in heading and flowering time. Here, we report identification of two Ae. tauschii accessions insensitive to short day length. Similarly to a loss or reduced degree of vernalization requirement, the photoperiod-insensitive mutations were found only in the early flowering sublineage (TauL1b) of Ae. tauschii. Quantitative trait locus (QTL) analyses using two F₂ mapping populations showed that a QTL for heading time on the long arm of chromosome 5D was related to the early heading phenotype of the photoperiod-insensitive accessions under short-day conditions. In the photoperiod-insensitive accession, expression patterns of two flowering-related genes were altered under short-day conditions compared with the patterns in photoperiod-sensitive accessions. This study indicates that analysis of natural variations in the Ae. tauschii population is useful to find novel genetic loci controlling agronomically important traits.     

Genetic Diversity of Farmers’Preferred Sorghum Accessions and Improved Lines from ICRISAT Reveal a Disconnect Between Innovation and Technology Transfer

The genetic diversity of 65 accessions of sorghum [Sorghum bicolor (L.) Moench] collected from various farmers and germplasm lines from ICRISAT-Kenya were analyzed. Simple sequence repeats (SSR) markers were used in order to determine the extent and distribution of its genetic diversity. Twenty-nine (29) SSRs markers were polymorphic and a total of 192 alleles were detected which showed diversity. The number of alleles per primer ranged from 2 to 17, with an average of 6.62. The range of polymorphism information content (PIC) ranged from 0.03 to 0.86, with total average of 0.82. According to the results analyzed, estimates of the mean allelic pattern across the two populations was generated; expected heterozygosity (He; 0.45, 0.54), average observed alleles (Na; 3.40, 6.20), number of private allele (0.23, 3.03), and Shannon information index (I; 0.85, 1.13) for farmer and ICRISAT-Kenya germplasm, respectively. The expected heterozygosity (He) varied from 0 to 0.26 with an average of 0.05. The Neighbor-joining phenogram based on Nei’s genetic distance grouped the 65 accessions into three main groups. The analysis of molecular variance (AMOVA) revealed that 99% of the total genetic variation was within accessions in a population whereas the genetic variation among populations in accessions accounted for 1% of the total genetic variation. Genetic diversity in ICRISAT sorghum material compared to the farmer’s collection suggested little infiltration of improved germplasm to the farmers.     

Phenotypic Variation in a Germplasm Collection of Pepper (<Emphasis Type="Italic">Capsicum chinense</Emphasis> Jacq.) from Korea

A total of 47 core collections of pepper (Capsicum chinense Jacq.) conserved in National Agrobiodiversity Center (NAC) were studied under field condition at Jeonju over two consecutive years (2015 and 2016). All accessions were characterized for their 14 qualitative and 16 quantitative characters. Results revealed that both qualitative and quantitative characters exhibited wide variation among the studied germplasm. Distribution of fruit characters (fruit length, width, and fruit wall thickness) among the accessions was positively skewed. Of the 47 accessions evaluated, 38.3% accessions had conical shaped fruits and mature fruit color was predominantly red (51.1%), orange (21.3%) and yellow (14.9%). Principal component analyses revealed that (i) 56.64% of the qualitative (fruit shape, color and fruit surface) variation and (ii) 89.42% of the quantitative (plant width, height and fruit maturity days) variation were explained by the first two components. Clustering revealed two groups and dendrogram revealed morphological variation among accessions. The phenotypic diversity exists in this core collections provide valuable information to improve agronomic traits in pepper breeding program.     

Pericarps retained in the tree canopy and stomatal abundance are components of resistance to husk spot caused by <Emphasis Type="Italic">Pseudocercospora macadamiae</Emphasis> in macadamia

Pseudocercospora macadamiae Beilharz, Mayers and Pascoe infects macadamia fruit via stomata causing husk spot disease. Information on the variability of fruit stomatal abundance, its association with diseased fruit pericarps (sticktights) that are retained in the tree canopy, and its influence on the husk spot intensity (incidence, severity and lesion number) among macadamia genotypes is lacking. We examined a total of 230 macadamia trees comprising 19 cultivars, 56 wild germplasm accessions and 40 breeding progeny, for the prevalence of sticktights and husk spot intensity over three production seasons. We observed a strong association between the prevalence of sticktights and disease intensity indicating its usefulness as a predictor of husk spot and as a useful phenotypic trait for husk spot resistance selection in breeding programmes. Similarly, stomatal abundance varied among macadamia genotypes, and a significant linear relationship (P < 0.001; 93%) was observed between fruit stomatal abundance and husk spot for all the macadamia genotypes analysed, confirming the utility of that trait for disease resistance screening. The genotypes were grouped into disease resistance groups. Correlations between fruit stomatal abundance, disease intensity and prevalence of sticktights revealed that the numbers of sticktights, and relative stomatal abundance were the main factors influencing the intensity of husk spot among macadamia genotypes. This is the first comprehensive study of natural variation of stomatal abundance in Macadamia species that reveals genetic variation, and provides relevant relationships with disease intensity and the prevalence of sticktights. The phenotypic plant traits indentified in this study may serve as selection tools for disease resistance screening in macadamia breeding programmes.     

Exploring the natural variation for reproductive thermotolerance in wild tomato species

Climate change has become a serious threat for crop productivity worldwide. The increased frequency of heat waves strongly affects reproductive success and thus yield for many crop species, implying that breeding for thermotolerant cultivars is critical for food security. Insight into the genetic architecture of reproductive heat tolerance contributes to our fundamental understanding of the stress sensitivity of this process and at the same time may have applied value. In the case of tomato (Solanum lycopersicum), germplasm screenings for thermotolerance have often used yield as the main measured trait. However, due to the complex nature of yield and the relatively narrow genetic variation present in the cultivated germplasm screened, there has been limited progress in understanding the genetic basis of reproductive heat tolerance. Extending the screening to wild accessions of related species that cover a range of climatic conditions might be an effective approach to find novel, more tolerant genetic resources. The purpose of this study was to provide insight into the sensitivity of individual reproductive key traits (i.e. the number of pollen per flower, pollen viability and style protrusion) to heat-wave like long-term mild heat (LTMH), and determine the extent to which genetic variation exists for these traits among wild tomato species. We found that these traits were highly variable among the screened accessions. Although no overall thermotolerant species were identified, several S. pimpinellifolium individuals outperformed the best performing cultivar in terms of pollen viability under LTMH. Furthermore, we reveal that there has been local adaptation of reproductive heat tolerance, as accessions from lower elevations and higher annual temperature are more likely to show high pollen viability under LTMH.     

Identification of quantitative trait loci controlling grain size and shape in the D genome of synthetic hexaploid wheat lines

Synthetic hexaploid wheat is an effective genetic resource for transferring agronomically important genes from Aegilops tauschii to common wheat. Wide variation in grain size and shape, one of the main targets for wheat breeding, has been observed among Ae. tauschii accessions. To identify the quantitative trait loci (QTLs) responsible for grain size and shape variation in the wheat D genome under a hexaploid genetic background, six parameters related to grain size and shape were measured using SmartGrain digital image software and QTL analysis was conducted using four F₂ mapping populations of wheat synthetic hexaploids. In total, 18 QTLs for the six parameters were found on five of the seven D-genome chromosomes. The identified QTLs significantly contributed to the variation in grain size and shape among the synthetic wheat lines, implying that the D-genome QTLs might be at least partly functional in hexaploid wheat. Thus, synthetic wheat lines with diverse D genomes from Ae. tauschii are useful resources for the identification of agronomically important loci that function in hexaploid wheat.     

Genomic analysis in three Hylocereus species and their progeny: evidence for introgressive hybridization and gene flow

Interest in vine cacti of the genus Hylocereus (Cactaceae) has grown markedly due to their high economic potential as exotic fruit crops. Thus, we investigate the genomic and genetic characteristics of 18 accessions belonging to three Hylocereus species, from which were produced eight progeny from self-pollination and 51 interspecific-homoploid and -interploid hybrids. We reported ploidy estimation, allele frequencies, polymorphic information content (PIC) and genetic relationships observed among the Hylocereus species and their progeny. The progeny were diploid, triploid, tetraploid, pentaploid, or hexaploid. Each primer combination used in this work amplified different sets of restriction fragments ranging from 74 to 102 bands. Among the total number of bands observed for the Hylocereus accessions and their progeny, 97.5 and 98.1 %, respectively, were polymorphic. The variability of PIC between primers, species and hybrids suggested high heterozygosity and gene flow between them. In addition, amplified fragment length polymorphism (AFLP) markers were used to successfully identify one of the H. megalanthus accessions beforehand as the unknown male progenitor of the allotriploid S-75. AFLP markers demonstrate the efficacy for assessing genetic relationships and introgression; and provide strong support for the pursuit of additional breeding programs of these fruit crop.     

Molecular characterization of South and East Asian melon, Cucumis melo L., and the origin of Group Conomon var. makuwa and var. conomon revealed by RAPD analysis

The genetic diversity and relationship among South and East Asian melon Cucumis melo L. were studied by using RAPD analysis of 69 accessions of melon from India, Myanmar, China, Korea, and Japan. The genetic diversity was large in India, and quite small in Group Conomon var. makuwa and var. conomon from East Asia, clearly indicating a decrease in genetic variation from India toward the east. Cluster analysis based on genetic distance classified 17 groups of accessions into two major clusters: cluster I comprising 12 groups of accessions from India and Myanmar and cluster II that included five groups of accessions of Group Conomon var. makuwa and var. conomon from East Asia. Cluster I was further divided into three subclusters, of which subclusters Ib and Ic included small- and large-seed type populations, respectively. Therefore, this division was based on their seed size, not cultivation area. The large-seed type from east India was differently included in the subcluster of small-seed type (Ib). A total of 122 plants of 69 accessions were classified into three major clusters and subclusters: clusters I and II comprised melon accessions mostly from India and Myanmar, and cluster III comprised Group Conomon var. makuwa and var. conomon from East Asia. The frequency of large- and small-seed types was different between clusters I and II, also indicating genetic differentiation between large- and small-seed types. One plant of the small-seed type from east India was differently included in cluster III, and two plants from east India were classified into subcluster IV. These results clearly showed that South Asian melon is genetically differentiated by their seed size, and that small-seed type melon in east India is closely related to Group Conomon var. makuwa and var. conomon.     

Mapping and use of QTLs controlling pod dehiscence in soybean

While the cultivated soybean, Glycine max (L.) Merr., is more recalcitrant to pod dehiscence (shattering-resistant) than wild soybean, Glycine soja Sieb. & Zucc., there is also significant genetic variation in shattering resistance among cultivated soybean cultivars. To reveal the genetic basis and develop DNA markers for pod dehiscence, several research groups have conducted quantitative trait locus (QTL) analysis using segregated populations derived from crosses between G. max accessions or between a G. max and G. soja accession. In the populations of G. max, a major QTL was repeatedly identified near SSR marker Sat_366 on linkage group J (chromosome 16). Minor QTLs were also detected in several studies, although less commonality was found for the magnitudes of effect and location. In G. max × G. soja populations, only QTLs with a relatively small effect were detected. The major QTL found in G. max was further fine-mapped, leading to the development of specific markers for the shattering resistance allele at this locus. The markers were used in a breeding program, resulting in the production of near-isogenic lines with shattering resistance and genetic backgrounds of Japanese elite cultivars. The markers and lines developed will hopefully contribute to the rapid production of a variety of shattering-resistant soybean cultivars.     

Fine mapping of the uniform immature fruit color gene u in cucumber (Cucumis sativus L.)

Mottled/uniform color at the flower end of immature fruit is a highly important external quality trait that affects the market value of cucumber. Genetic analysis of different F₂ and backcross populations revealed that one single recessive gene, u (uniform immature fruit color), determines the uniform immature fruit color trait in cucumber. Based on earlier studies, the u locus is located on chromosome 5 (Chr. 5). By combining bulked segregant analysis using 60 published molecular markers on Chr. 5, we found that eight markers are polymorphic and are linked to the u locus. In addition, we developed five new relevant polymorphic simple sequence repeat (SSR) markers between markers SSR16203 and SSR15818. Subsequently, the F₂ population (477 individuals) from the cross of S06 (uniform fruit color line) × S94 (mottled fruit color line) was used for fine mapping of the u gene. The u gene was mapped to a 313.2-kb region between markers SSR10 and SSR27, at a genetic distance of 0.8 and 0.5 cM, respectively. Moreover, validity analysis of the codominant markers SSR10 and SSR27 was performed using 50 lines with mottled/uniform fruit color, demonstrating that these two SSR markers can be used for marker-assisted selection of the mottled/uniform fruit color trait in cucumber breeding. The results of this study will facilitate the cloning of the u gene.     

RFLP analysis of genetic variation in species of section Arachis, genus Arachis (Leguminosae)

Four A-genome species of the genus Arachis (A. cardenasii, A. correntina, A. duranensis, A. kempff-mercadoi), three B genomes species (A. batizocoi, A. ipaënsis and A. magna),the AABB allotetraploid A. hypogaea (cultivated peanut) and introgression lines resulting from a cross between A. hypogaea and A. cardenasii were analyzed by RFLP. The A genome species (cytologically characterized by the presence of a small chromosome pair ‘A’) were closely similar to each other and shared a large number of restriction fragments. In contrast, the B genome species differed more from one another and shared few fragments. The results of this study indicate that the absence of the small chromosome pair is not a good criterion for grouping species of section Arachis as B genome species, since their genome might be quite distinct from the B genome of A. hypogaea.The lowest genetic variation was detected within accessions of A. duranensis (17 accessions), followed by A. batizocoi (4 accessions) and A. cardenasii (9 plants of accession GKP 10017).The high level of genetic variation found in A. cardenasii might indicate that not all accessions of wild species of Arachis are autogamous, as reported for A. hypogaea.     

Genetic diversity for agronomic and fiber traits in day-neutral accessions derived from primitive cotton germplasm

Upland cotton (Gossypium hirsutumL) is an important crop that is cultivated in warm climates through-out the world. Agronomic performance and fiber quality must continually be improved if cotton is to maintain economic viability. Primitive ancestors of cotton contain diversity for trait improvement; however, many of these accessions have a short-day flowering response (photoperiodic) and are not readily useable in breeding programs. In this study, 114 day-neutral derived primitive germplasm lines were evaluated in field trials for two years. Agronomic and fiber trait data were collected and analyzed. Variance components, genotypic values, and genotypic correlations were calculated. Genotypic effects for all traits studied made significant contributions to the phenotypic variation indicating genetic diversity among these lines. The predicted genotypic values showed a wide range of variation for agronomic and fiber traits. Weak genotypic correlations were found between yield and 2.5% span length and fiber strength, two important fiber traits. Although these day-neutral derived accessions had lower lint percentage, they had improved fiber length, strength, micronaire, and comparable yields with two commercial cultivars. Thus, these day-neutral derived accessions are sources of genetic variation that when used in breeding programs offer the potential to improve important traits and expand genetic diversity.Contribution of the USDA-ARS in cooperation with the Mississippi Agric. and Forestry Exp. Stn. Mention of trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by USDA, ARS and does not imply its approval to the exclusion of other products or vendors that may also be suitable.