Genetic analysis of Verticillium wilt resistance in a backcross inbred line population and a meta-analysis of quantitative trait loci for disease resistance in cotton

Abstract

BackgroundVerticillium wilt (VW) and Fusarium wilt (FW), caused by the soil-borne fungi Verticillium dahliae and Fusarium oxysporum f. sp. vasinfectum, respectively, are two most destructive diseases in cotton production worldwide. Root-knot nematodes (Meloidogyne incognita, RKN) and reniform nematodes (Rotylenchulus reniformis, RN) cause the highest yield loss in the U.S. Planting disease resistant cultivars is the most cost effective control method. Numerous studies have reported mapping of quantitative trait loci (QTLs) for disease resistance in cotton; however, very few reliable QTLs were identified for use in genomic research and breeding.ResultsThis study first performed a 4-year replicated test of a backcross inbred line (BIL) population for VW resistance, and 10 resistance QTLs were mapped based on a 2895 cM linkage map with 392 SSR markers. The 10 VW QTLs were then placed to a consensus linkage map with other 182 VW QTLs, 75 RKN QTLs, 27 FW QTLs, and 7 RN QTLs reported from 32 publications. A meta-analysis of QTLs identified 28 QTL clusters including 13, 8 and 3 QTL hotspots for resistance to VW, RKN and FW, respectively. The number of QTLs and QTL clusters on chromosomes especially in the A-subgenome was significantly correlated with the number of nucleotide-binding site (NBS) genes, and the distribution of QTLs between homeologous A- and D- subgenome chromosomes was also significantly correlated.ConclusionsTen VW resistance QTL identified in a 4-year replicated study have added useful information to the understanding of the genetic basis of VW resistance in cotton. Twenty-eight disease resistance QTL clusters and 24 hotspots identified from a total of 306 QTLs and linked SSR markers provide important information for marker-assisted selection and high resolution mapping of resistance QTLs and genes. The non-overlapping of most resistance QTL hotspots for different diseases indicates that their resistances are controlled by different genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1682-2) contains supplementary material, which is available to authorized users.

Quantitative trait loci analysis of Verticillium wilt resistance in interspecific backcross populations of Gossypium hirsutum × Gossypium barbadense

“…5, Table 2). 7 QTL hotspot regions (c5-VW-Hotspot-2, c7-VW-Hotspot-1, c7-VW-Hotspot-2, c8-VW-Hotspot-1, c19-VW-Hotspot-1, c21-VW-Hotspot-1 and c26-VW-Hotspot-1) were consistent with those identified previously by Zhang et al and Said et al [13, 34] (Table 2), and the other ten were new, unreported hotspot regions. Two QTL hotspot regions were on C5, C7, C9 and C19, respectively.…”

“…5, Table 2). Of them, 7 QTL hotspot regions were consistent with those identified previously by Zhang et al and Said et al [13, 34] (Table 2) and another 10 were new, unreported hotspot regions. 36 (75 %) QTLs from this paper were distributed in 15 hotspot regions, of which 29 QTLs were in 12 hotspot regions and were all from G. barbadense (Table 3).…”

“…of QTLsNo. of QTLs in this paperReported previouslyc3-VW-Hotspot-1C316–28 cM76c5-VW-Hotspot-1C528–43 cM75c5-VW-Hotspot-2C547–68 cM52Zhang et al 2015 [13] and Said et al 2015 [34]c7-VW-Hotspot-1C743–59 cM41Zhang et al 2015 [13]c7-VW-Hotspot-2C764–85 cM53Zhang et al 2015 [13]c8-VW-Hotspot-1C817–34 cM82Zhang et al 2015 [13]c9-VW-Hotspot-1C955–85 cM61c9-VW-Hotspot-2C9124–147 cM50c12-VW-Hotspot-1C1217–26 cM43c14-VW-Hotspot-1C1426–43 cM53c15-VW-Hotspot-1C1542–63 cM63c17-VW-Hotspot-1C1711–36 cM41c19-VW-Hotspot-1C191–26 cM50Zhang et al 2015 [13]c19-VW-Hotspot-2C19120–132 cM41c20-VW-Hotspot-1C201–26 cM41c21-VW-Hotspot-1C2130–44 cM61Zhang et al 2015 [13]c26-VW-Hotspot-1C2654–79 cM93Zhang et al 2015 [13] …”

“…For example, Zhang et al detected QTLs for VW resistance based on a 392 SSR polymorphic loci linkage map covering 2895 cM or about 57.90 % of the cotton genome using the BIL population of SG 747 × Giza 75 [13]. Fang et al constructed a 292-marker genetic linkage map for the BIL population of SG 747 × Pima S-7 [15].…”

“…However, sources of VW resistance in cotton are very limited and no source of heritable immunity has been found in Upland cotton [4, 9]. Many G. barbadense genotypes are known to carry high levels of resistance to VW [4, 10, 11], but its resistance has not been successfully transferred into commercial Upland cotton due to hybrid breakdown except for introgressed breeding lines [4, 12, 13]. Using conventional breeding, breeders have made interspecific crosses between Upland cotton and sea-island cotton to improve the VW resistance of Upland cotton for many years, but no breakthrough has been reported because of the negative genetic correlation between lint yield and fiber quality, between lint yield and disease resistance, as well as linkage drag and hybrid breakdown [14].…”