Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (<i>Citrullus lanatus</i> [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data

Abstract Cultivated peanut (Arachis hypogaea L.) is rich in edible oil and protein, which is widely planted around the world as an oil and cash crop. However, aflatoxin contamination seriously affects the quality safety of peanut, hindering the development of peanut industry and threatening consumers’ health. Breeding peanut varieties with resistance to Aspergillus flavus infection is important for control the aflatoxin contamination, and understanding of the genetic basis of resistance is vital to its genetic enhancement. In this study, we report the QTL mapping of resistance to A. flavus infection of a well-known resistant variety J11. A recombination inbred line (RIL) population was constructed by crossing a susceptible variety Zhonghua 16 and J11. Through whole-genome resequencing, a genetic linkage map was constructed with 2,802 recombination bins and an average inter-bin distance of 0.58 cM. Combined with phenotypic data of infection index in four consecutive years, six novel resistant QTLs were identified and they explained 5.03-10.87% phenotypic variances. The favorable alleles of five QTLs were from J11 while that of one QTL were from Zhonghua 16. The pyramiding of these favorable alleles significantly improved the resistance to A. flavus infection. These results could contribute greatly to understanding of genetic basis of A. flavus resistance and could be meaningful in further resistance improvement in peanut.

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Construction of a genetic linkage map of watermelon (Citrullus lanatus) using CAPS and SSR markers and QTL analysis for fruit quality traits

Scientia Horticulturae ◽

10.1016/j.scienta.2016.01.004 ◽

2016 ◽

Vol 202 ◽

pp. 25-31 ◽

Cited By ~ 18

Author(s):

Yao Cheng ◽

Feishi Luan ◽

Xuezheng Wang ◽

Peng Gao ◽

Zicheng Zhu ◽

...

Keyword(s):

Linkage Map ◽

Ssr Markers ◽

Fruit Quality ◽

Qtl Analysis ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Citrullus Lanatus ◽

Quality Traits ◽

Fruit Quality Traits

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High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping QTLs of Resistance to Aspergillus flavus Infection in Peanut

Frontiers in Plant Science ◽

10.3389/fpls.2021.745408 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yifei Jiang ◽

Huaiyong Luo ◽

Bolun Yu ◽

Yingbin Ding ◽

Yanping Kang ◽

...

Keyword(s):

Linkage Map ◽

Aspergillus Flavus ◽

Genetic Linkage ◽

Genetic Basis ◽

Genetic Linkage Map ◽

Aflatoxin Contamination ◽

Whole Genome ◽

Genome Resequencing ◽

Favorable Alleles ◽

Whole Genome Resequencing

The cultivated peanut (Arachis hypogaea L.), which is rich in edible oil and protein, is widely planted around the world as an oil and cash crop. However, aflatoxin contamination seriously affects the quality safety of peanuts, hindering the development of the peanut industry and threatening the health of consumers. Breeding peanut varieties with resistance to Aspergillus flavus infection is important for the control of aflatoxin contamination, and understanding the genetic basis of resistance is vital to its genetic enhancement. In this study, we reported the quantitative trait locus (QTL) mapping of resistance to A. flavus infection of a well-known resistant variety, J11. A mapping population consisting of 200 recombinant inbred lines (RILs) was constructed by crossing a susceptible variety, Zhonghua 16, with J11. Through whole-genome resequencing, a genetic linkage map was constructed with 2,802 recombination bins and an average inter-bin distance of 0.58 cM. Combined with phenotypic data of an infection index in 4 consecutive years, six novel resistant QTLs with 5.03–10.87% phenotypic variances explained (PVE) were identified on chromosomes A05, A08, B01, B03, and B10. The favorable alleles of five QTLs were from J11, while that of one QTL was from Zhonghua 16. The combination of these favorable alleles significantly improved resistance to A. flavus infection. These results could contribute greatly to the understanding of the genetic basis of A. flavus resistance and could be meaningful in the improvement of further resistance in peanuts.

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A genetic linkage map for watermelon derived from a testcross population: (Citrullus lanatus var. citroides × C. lanatus var. lanatus) × Citrullus colocynthis

Theoretical and Applied Genetics ◽

10.1007/s00122-001-0860-6 ◽

2002 ◽

Vol 105 (4) ◽

pp. 555-563 ◽

Cited By ~ 30

Author(s):

A. Levi ◽

C. Thomas ◽

T. Joobeur ◽

X. Zhang ◽

A. Davis

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Citrullus Lanatus ◽

Citrullus Colocynthis

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A Genetic Linkage Map for Watermelon Derived from Recombinant Inbred Lines

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.129.2.0237 ◽

2004 ◽

Vol 129 (2) ◽

pp. 237-243 ◽

Cited By ~ 16

Author(s):

Renbing Zhang ◽

Yong Xu ◽

Ke Yi ◽

Haiying Zhang ◽

Ligong Liu ◽

...

Keyword(s):

Linkage Map ◽

Recombinant Inbred ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Citrullus Lanatus ◽

Average Distance ◽

Recombinant Inbred Lines ◽

Plant Introduction ◽

Inter Simple Sequence Repeat ◽

Inbred Lines

A genetic linkage map was constructed for watermelon using 117 recombinant inbred lines (RILs) (F2S7) descended from a cross between the high quality inbred line 97103 [Citrullus lanatus var. lanatus (Thunb.) Matsum. & Nakai] and the Fusarium wilt (races 0, 1, and 2) resistant U.S. Plant Introduction (PI) 296341 (C. lanatus var. citroides). The linkage map contains 87 randomly amplified polymorphic DNA (RAPD) markers, 13 inter simple sequence repeat (ISSR) markers, and four sequenced characterized amplified region (SCAR) markers. The map consists of 15 linkage groups. Among them are a large linkage group of 31 markers covering a mapping distance of 277.5 cM, six groups each with 4 to 12 markers covering a mapping distance of 51.7 to 172.2 cM, and eight small groups each with 2-5 markers covering a mapping distance of 7.9 to 46.4 cM. The map covers a total distance of 1027.5 cM with an average distance of 11.7 cM between two markers. The map is useful for the further development of quantitative trait loci (QTLs) affecting fruit qualities and for identification of genes conferring resistance to Fusarium wilt (races 0, 1 and 2). The present map can be used for further construction of a reference linkage map for watermelon based on an immortalized mapping population with progenies homozygous for most gene loci.

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DNA Markers from Different Linkage Regions of Watermelon Genome Useful in Differentiating among Closely Related Watermelon Genotypes

HortScience ◽

10.21273/hortsci.42.2.210 ◽

2007 ◽

Vol 42 (2) ◽

pp. 210-214 ◽

Cited By ~ 9

Author(s):

Amnon Levi ◽

Claude E. Thomas

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Fragment Length Polymorphism ◽

Citrullus Lanatus ◽

Plant Introduction ◽

Polymorphic Markers ◽

Linkage Groups ◽

Breeding Lines ◽

Srap Markers

A genetic linkage map was previously constructed for watermelon using a wide testcross population [{Plant Accession Griffin 14113; Citrullus lanatus var. citroides (L.H. Baiely) Mansf.} × the watermelon cultivar New Hampshire Midget; NHM {(Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus)} × United States Plant Introduction (PI) 386015 {Citrullus colocynthis (L.) Schrad.}]. One-hundred forty-six markers [randomly amplified polymorphic DNA (RAPD), intersimple sequence repeat (ISSR), amplified fragment length polymorphism (AFLP), and sequence-related amplified polymorphism (SRAP) markers] unique to NHM and representing different linkage groups on the map were tested for polymorphism among 24 watermelon cultivars limited in genetic diversity. Five (9.4%) of 53 RAPD, six (40.0%) of 15 ISSR, 30 (81.0%) of 37 AFLP, and 33 (80.5%) of 41 SRAP markers tested produced polymorphism among the 24 cultivars. The polymorphic markers used in this study are scattered throughout the watermelon genome. However, a large number (19 of the 30) of AFLP markers clustered on one linkage group on the map. The SRAP markers proved to be most effective in producing polymorphism and in representing different linkage regions of watermelon genome. The polymorphic markers represent all 10 large linkage groups and five of the nine small linkage groups (altogether 15 of 19 linkage groups) of the genetic linkage map constructed so far for watermelon. These polymorphic markers can be useful in DNA fingerprinting of cultivars, in testing seed purity of breeding lines, and in identifying triploid (seedless) hybrid watermelons derived from crosses between closely related tetraploid and diploid lines.

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