Refining of the egusi locus in watermelon using KASP assays

Paudel, Lucky; Clevenger, Josh; McGregor, Cecilia

doi:10.1016/j.scienta.2019.108665

Cited by 15 publications

(17 citation statements)

References 21 publications

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“…Among the different platforms, the KASP assay is a promising technology for high throughput SNP genotyping (Ayalew et al, 2019 ). The SNP-based KASP assays for MAS have been developed for many traits in cucurbits (Paudel et al, 2019 ; Cao et al, 2021 ; Kahveci et al, 2021 ). The polymorphic KASP assays have been used in the present investigation to develop a partial genetic linkage map of 40.3 cM and the Cphl-1 locus was delimited between two markers Cp_3430407 and Cp_3498687.…”

Section: Discussionmentioning

confidence: 99%

Identification of single major QTL and candidate gene(s) governing hull-less seed trait in pumpkin

et al. 2022

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The hull-less pumpkin (Cucurbita pepo) seed does not require de-hulling before use for human consumption, as a result highly preferred by the oil, nut, and baking industries. In hull-less seeds, a single recessive gene is responsible for the absence of outer thick seed coat layers; however, the genomic region and gene(s) controlling the trait are unclear to date. In this study, four crosses attempted to derive F2 and backcross populations confirmed the single recessive gene inheritance of hull-less seed trait in populations adapted to the sub-tropical climate. The candidate genomic region for hull-less seed trait was identified through the BSA-QTLseq approach using bulks of F2:3 progenies from a cross of HP111 (hulled) and HLP36 (hull-less). A novel genomic region on chromosome 12 ranging from 1.80 to 3.86 Mb was associated with the hull-less seed trait. The re-sequencing data identified a total of 396 SNPs within this region and eight were successfully converted into polymorphic KASP assays. The genotyping of segregating F2 (n = 160) with polymorphic KASP assays resulted in a 40.3 cM partial linkage map and identified Cp_3430407 (10 cM) and Cp_3498687 (16.1 cM) as flanking markers for hull-less locus (Cphl-1). These flanking markers correspond to the 68.28 kb region in the reference genome, and the marker, Cp_3430407 successfully predicted the genotype in 93.33% of the C. pepo hull-less germplasm lines, thus can be used for marker-assisted selection in parents polymorphic for the hull-less seed trait. The Cphl-1-linked genomic region (2.06 Mb) encompasses a total of 182 genes, including secondary cell wall and lignin biosynthesis-related transcriptional factors viz., “NAC” (Cp4.1LG12g04350) and “MYB” (Cp4.1LG12g03120). These genes were differentially expressed in the seeds of hulled and hull-less genotypes, and therefore could be the potential candidate genes governing the hull-less seed trait in pumpkin.

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Section: Discussionmentioning

confidence: 99%

Identification of single major QTL and candidate gene(s) governing hull-less seed trait in pumpkin

et al. 2022

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“…In our study, additional markers that spanned the QTL-seq identified loci were mapped in the entire 17S28 F 2 population, resulting in the confirmation of BER3.1 and BER11.1. The other QTL on ch1 and ch8 were false positives, which is not uncommon in QTL-seq experiments (Paudel et al 2019b). Generally for QTL-Seq, the bulk size needs to be composed of at least 15% of the total F 2 population to detect minor QTL that explain less than 10% of the percentage of total phenotypic variation explained (Takagi et al 2013).…”

Section: Discussionmentioning

confidence: 99%

Identification of blossom-end rot loci using joint QTL-seq and linkage-based QTL mapping in tomato

et al. 2021

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Key message Blossom-End Rot is Quantitatively Inherited and Maps to Four Loci in Tomato. Abstract Blossom-end rot (BER) is a devastating physiological disorder that affects tomato and other vegetables, resulting in significant crop losses. To date, most studies on BER have focused on the environmental factors that affect calcium translocation to the fruit; however, the genetic basis of this disorder remains unknown. To investigate the genetic basis of BER, two F2 and F3:4 populations along with a BC1 population that segregated for BER occurrence were evaluated in the greenhouse. Using the QTL-seq approach, quantitative trait loci (QTL) associated with BER Incidence were identified at the bottom of chromosome (ch) 3 and ch11. Additionally, linkage-based QTL mapping detected another QTL, BER3.1, on ch3 and BER4.1 on ch4. To fine map the QTLs identified by QTL-seq, recombinant screening was performed. BER3.2, the major BER QTL on ch3, was narrowed down from 5.68 to 1.58 Mbp with a 1.5-LOD support interval (SI) corresponding to 209 candidate genes. BER3.2 colocalizes with the fruit weight gene FW3.2/SlKLUH, an ortholog of cytochrome P450 KLUH in Arabidopsis. Further, BER11.1, the major BER QTL on ch11, was narrowed down from 3.99 to 1.13 Mbp with a 1.5-LOD SI interval comprising of 141 candidate genes. Taken together, our results identified and fine mapped the first loci for BER resistance in tomato that will facilitate marker-assistant breeding not only in tomato but also in many other vegetables suffering for BER.

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“…After this, one of the fluor-labelled oligo that was quenched until now binds as a tail to the corresponding amplified allele, generating a fluorescent signal. KASP assays have been extensively used in different crops, mainly cereals, becoming very helpful for MAS in wheat [ 90 , 91 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 ], barley [ 100 ], rice [ 101 , 102 , 103 , 104 ], sorghum [ 105 ], pea [ 106 ], watermelon [ 107 , 108 ], faba bean [ 109 ], tomato [ 110 , 111 ], and Brassica oleracea (cabbage, broccoli, kohlrabi, and Chinese kale [ 112 ]).…”

Section: Exploring Biodiversity: Searching For Outstanding Materialsmentioning

confidence: 99%

Applications of Genomic Tools in Plant Breeding: Crop Biofortification

Medina-Lozano

Díaz

2022

IJMS

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Crop breeding has mainly been focused on increasing productivity, either directly or by decreasing the losses caused by biotic and abiotic stresses (that is, incorporating resistance to diseases and enhancing tolerance to adverse conditions, respectively). Quite the opposite, little attention has been paid to improve the nutritional value of crops. It has not been until recently that crop biofortification has become an objective within breeding programs, through either conventional methods or genetic engineering. There are many steps along this long path, from the initial evaluation of germplasm for the content of nutrients and health-promoting compounds to the development of biofortified varieties, with the available and future genomic tools assisting scientists and breeders in reaching their objectives as well as speeding up the process. This review offers a compendium of the genomic technologies used to explore and create biodiversity, to associate the traits of interest to the genome, and to transfer the genomic regions responsible for the desirable characteristics into potential new varieties. Finally, a glimpse of future perspectives and challenges in this emerging area is offered by taking the present scenario and the slow progress of the regulatory framework as the starting point.

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Refining of the egusi locus in watermelon using KASP assays

Cited by 15 publications

References 21 publications

Identification of single major QTL and candidate gene(s) governing hull-less seed trait in pumpkin

Identification of single major QTL and candidate gene(s) governing hull-less seed trait in pumpkin

Identification of blossom-end rot loci using joint QTL-seq and linkage-based QTL mapping in tomato

Applications of Genomic Tools in Plant Breeding: Crop Biofortification

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