Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar ‘Koshihikari’

Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar ‘Koshihikari’ was performed to extract regions containing large indels (10–51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between ‘Koshihikari’ and other diverse cultivars, we subtracted the indel regions detected in ‘Koshihikari’ from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including ‘Khao Nam Jen’ as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.     

Comparative genetic analysis of field resistance to downy mildew in the lettuce cultivars ‘Grand Rapids’ and ‘Iceberg’

Downy mildew on lettuce is currently controlled using host resistance genes (Dm genes) that confer race-specific resistance in seedlings. Field resistance (FR) that is active in adult plants but not seedlings was identified in the cvs. Grand Rapids and Iceberg. The goal of our study was to evaluate the utility of Grand Rapids as a source of novel Bremia resistance alleles, particularly in comparison with Iceberg. To measure FR, downy mildew symptoms were evaluated following natural infection in field experiments. The responses of Grand Rapids and Iceberg were similar in many respects. Although both cultivars had a small percentage of plants exhibiting disease symptoms, the average disease ratings were as low as for cultivars with effective Dm genes. We observed no evidence for race specificity. FR was effective over 3 years of our study, despite documented variation within pathogen populations. Both cultivars lacked all known seedling resistance genes except Dm13, which was not responsible for the resistance observed in field experiments. Similar segregation of FR was observed in F₂ populations for both Grand Rapids and Iceberg. The presence of highly susceptible families within Grand Rapids × Iceberg populations suggested the presence of at least one unique resistance allele in each cultivar. Preliminary genetic analysis of FR from Grand Rapids revealed a high estimate of narrow-sense heritability that suggested simple inheritance, but single gene models did not fit the observed data. Our results suggest that Grand Rapids may represent an underutilized resource for controlling downy mildew in lettuce.     

Identification of major QTLs associated with stable resistance of tomato cultivar ‘Hawaii 7996’ to Ralstonia solanacearum

Bacterial wilt caused by Ralstonia solanacearum is one of the most devastating diseases of tomato. Tomato cultivar ‘Hawaii 7996’ has been shown to have stable resistance against different strains under different environments. This study aimed to locate quantitative trail loci (QTLs) associated with stable resistance using 188 recombinant inbred lines (RILs) derived from ‘Hawaii 7996’ and ‘West Virginia 700.’ A new linkage map with good genome coverage was developed, mainly using simple sequence repeat markers developed from anchored bacterial artificial chromosome or scaffold sequences of tomato. The population was evaluated against phylotype I and phylotype II strains at seedling stage or in the field in Indonesia, Philippines, Taiwan, Thailand, and Reunion. Two major QTLs were identified to be associated with stable resistance. Bwr-12, located in a 2.8-cM interval of chromosome 12, controlled 17.9–56.1 % of total resistance variation. The main function of Bwr-12 was related to suppression of internal multiplication of the pathogen in the stem. This QTL was not associated with resistance against race 3-phylotype II strain. Bwr-6 on chromosome 6 explained 11.5–22.2 % of the phenotypic variation. Its location differed with phenotype datasets and was distributed along a 15.5-cM region. The RILs with the resistance allele from both Bwr-12 and Bwr-6 had the lowest disease incidence, which was significantly lower than the groups with only Bwr-12 or Bwr-6. Our studies confirmed the polygenic nature of resistance to bacterial wilt in tomato, and that stable resistance in ‘Hawaii 7996’ is mainly associated with Bwr-6 and Bwr-12.     

Inheritance of the virgata pattern of partly colored seed coats in ‘Early Giant’ common bean

The inheritance of the virgata pattern of partly colored seed coats found in common bean (Phaseolus vulgaris L.) Early Giant (EG) was studied by a series of test crosses with line 5-593 and genetic stocks developed by backcrossing selected genes into the recurrent parent 5-593, a Florida dry bean breeding line with a self-colored, black seed coat with genotype T Z Bip P [C r] J G B V Rk. Analysis of the F₂ from the cross EG × 5-593 led to the hypothesis that the virgata pattern of EG has genotype t z bip^vgt, where vgt stands for virgata. The test cross EG × t z virgarcus BC₃ 5-593 confirmed the hypothesis that EG carries t z from data recorded in F₁, F₂, and 27 F₃ progenies from randomly selected F₂ plants. The F₃ segregation was also consistent with the hypothesis that a single recessive gene converts virgarcus into virgata. The test cross EG × t z bip bipunctata BC₃ 5-593 failed to show genetic complementation in F₁ progeny, and the F₂ segregated 3:1 for the parental phenotypes virgata and bipunctata, respectively. Including previously published data, all possible crosses were made among bipunctata, virgata, and virgarcus parents, supporting a multiple allelic series at Bip. We propose the gene symbol bip^vgt for the new allele at Bip, where the allelic series has the order of gene dominance Bip > bip^vgt > bip. Based on test crosses, the complete seed-coat color and pattern genotype of EG is tz bip^vgt P [C r] J G B v^lae rk^d.     

Prestorage application of high carbon dioxide combined with controlled atmosphere storage as a dual approach to control Botrytis cinerea in organic ‘Flame Seedless’ and ‘Crimson Seedless’ table grapes

Pre-storage application of 40% CO₂ at 0 °C for 24 or 48 h and controlled atmosphere (12% O₂ + 12% CO₂) storage at 0 °C for up to eight weeks on decay control and quality of organic ‘Flame Seedless’ and ‘Crimson Seedless’ table grapes were studied as a postharvest disease control alternative. To simulate different potential field conditions, these organic treatments were applied to organic-grown grapes that were naturally infected (without inoculation), surface inoculated (berries inoculated by spraying with a conidia suspension), and nesting inoculated (clusters inoculated by placing in the middle an artificially infected berry) with the pathogen Botrytis cinerea, the cause of grape gray mold. Under these three conditions, a 40% CO₂ for 48 h pre-storage treatment followed by controlled atmosphere reduced the gray mold incidence from 22% to 0.6% and from 100% to 7.4% after four and seven weeks, respectively. High CO₂ pre-storage alone limited botrytis incidence in both naturally and artificially infected grapes, but was more effective when combined with CA. These treatments did not affect visual or sensory fruit quality. Exposure to high CO₂ for 24 or 48 h effectively inhibited mycelial growth of B. cinerea in PDA plates incubated at 22 °C for up to 72 h. Conidia germination in PDA plates was reduced ∼60% after 12 h incubation. In vitro studies demonstrated a fungistatic effect, but further studies on the mechanism of action could improve treatment performance. This novel high CO₂ initial fumigation followed by controlled atmosphere during storage or transportation could be a commercially feasible alternative for postharvest handling of organic and conventional table grapes. Our results encourage validating this combined physical treatment in other cultivars and under commercial conditions.     

Identification of QTL associated with durable adult plant resistance to stem rust race Ug99 in wheat cultivar ‘Pavon 76’

Stem rust of wheat, caused by Puccinia graminis f. sp. tritici, was under control worldwide for over 30 years by utilizing genetic resistance. The emergence of stem rust in 1998 in eastern Africa in form of race Ug99 and its evolving variants with virulence to many resistance genes were recognized as potential threats to wheat production. In this study we identified genomic regions contributing to putatively durable, adult plant resistance (APR) to wheat stem rust. A recombinant inbred line (RIL) population of 298 lines was previously developed at CIMMYT from a cross between ‘Avocet S’ and ‘Pavon 76’. Pavon 76 has been described to carry APR to stem rust. Avocet S carries the race-specific resistance gene Sr26. A subset of RILs without Sr26 segregated for APR to stem rust race Ug99 when evaluated in Kenya for three years. Single year and joint year analysis by inclusive composite interval mapping using 450 DArT markers identified five quantitative trait loci (QTL) that contributed to the resistance of wheat to stem rust race Ug99. Three of these, including QSr.cim-3B, which probably represents the Sr2 gene, were contributed by Pavon 76 whereas the remaining two QTL were contributed by Avocet S. QSr.cim-3B, or putatively Sr2, on chromosome arm 3BS explained 32 % of the phenotypic variation while the additional QTL in Pavon contributed 24 and 20 %, respectively. Two QTL from Avocet S explained 8 and 6 % of phenotypic variance, respectively. A combination of APR QTL from the two parents resulted in transgressive segregants expressing higher levels of resistance than Pavon 76. Our results indicate that it is possible to accumulate several minor resistance genes each with a small to intermediate effect resulting in a variety that exhibits negligible disease levels even under high stem rust pressure.     

Physiology of fresh-cut ‘Galia’ (Cucumis melo var. reticulatus) from ripe fruit treated with 1-methylcyclopropene

‘Galia’ (Cucumis melo var. reticulatus L. Naud. cv. Galia) fruit were harvested at the three-quarter slip stage and treated with 1 μL L⁻¹ 1-methylcyclopropene (1-MCP) at 20 °C for 24 h. The fruit were processed and stored as fresh-cut cubes and intact fruit for 10 d at 5 °C. Ethylene production of fresh-cut cubes was approximately 4–5-fold higher than intact fruit at day 1. Afterward, the ethylene production of fresh-cut cubes declined significantly whereas that of intact fruit remained relatively constant at about 0.69–1.04 ng kg⁻¹ s⁻¹. 1-MCP delayed mesocarp softening in both fresh-cut and intact fruit and the symptoms of watersoaking in fresh-cut fruit. Continuously stored fresh-cut cubes and cubes derived from intact fruit not treated with the ethylene antagonist softened 27% and 25.6%, respectively, during 10 d storage at 5 °C while cubes derived from 1-MCP-treated fruit softened 9% and 17%, respectively. Fresh-cut tissue from 1-MCP-treated fruit exhibited slightly reduced populations of both total aerobic organisms and Enterobacterium, although the differences did not appear to be sufficient to explain the differences in keeping quality between 1-MCP-treated and control fruit. Based primarily on firmness retention and reduced watersoaking, 1-MCP treatment deferred loss of physical deterioration of fresh-cut ‘Galia’ cubes at 5 °C by 2–3 d compared with controls.     

Genetic Diversity of Ethiopian Tef [(Eragrostis tef (Zucc.) Trotter] Released and Selected Farmers’ Varieties along with Two Wild Relatives as Revealed by Microsatellite Markers

Journal of Crop Science and Biotechnology - Knowledge on the extent and pattern of diversity in crop species is a precondition for any crop improvement as it helps breeders in determining apt...     

Allocation of a powdery mildew resistance locus to the chromosome arm 6RL of <Emphasis Type="Italic">Secale cereale</Emphasis> L. cv. ‘Jingzhouheimai’

Chinese cultivar Jingzhouheimai of Secale cereale L. confers resistance to several important wheat diseases, making it a useful resource for wheat improvement. Octoploid amphiploid (2n = 8x = 56; AABBDDRR) was synthesized by hybridization of Jingzhouheimai with hexaploid wheat landrace Huixianhong and doubling of the F1 chromosome number. This amphiploid was backcrossed to the wheat parent to produce wheat-rye chromosome addition lines. The existing six disomic addition lines (all except 6R) were screened with 16 rye-specific DNA markers and three putative markers for 6R were identified. These markers were used in selection of chromosome 6R addition lines, confirmed by the genomic in situ hybridization (GISH). In this manner, seven monosomic 6R and five disomic addition were selected, as well as one mono-telosomic 6RS addition, one mono-telosomic and one ditelosomic 6RL additions. In turn these 6R addition lines were used to develop additional 15 6R-specific markers of which six were allocated to the arm 6RS and nine to 6RL. Screening for the powdery mildew resistance identified chromosome arm 6RL as the carrier of the resistance locus. Therefore, DNA markers identified as specific to the 6RL arm can be used to monitor the introgression of the resistance locus into wheat.