QTL Analysis for Transgressive Resistance to Root-Knot Nematode in Interspecific Cotton (Gossypium spp.) Progeny Derived from Susceptible Parents

Abstract

The southern root-knot nematode (RKN, Meloidogyne incognita) is a major soil-inhabiting plant parasite that causes significant yield losses in cotton (Gossypium spp.). Progeny from crosses between cotton genotypes susceptible to RKN produced segregants in subsequent populations which were highly resistant to this parasite. A recombinant inbred line (RIL) population of 138 lines developed from a cross between Upland cotton TM-1 (G. hirsutum L.) and Pima 3–79 (G. barbadense L.), both susceptible to RKN, was used to identify quantitative trait loci (QTLs) determining responses to RKN in greenhouse infection assays with simple sequence repeat (SSR) markers. Compared to both parents, 53.6% and 52.1% of RILs showed less (P<0.05) root-galling index (GI) and had lower (P<0.05) nematode egg production (eggs per gram root, EGR). Highly resistant lines (transgressive segregants) were identified in this RIL population for GI and/or EGR in two greenhouse experiments. QTLs were identified using the single-marker analysis nonparametric mapping Kruskal-Wallis test. Four major QTLs located on chromosomes 3, 4, 11, and 17 were identified to account for 8.0 to 12.3% of the phenotypic variance (R2) in root-galling. Two major QTLs accounting for 9.7% and 10.6% of EGR variance were identified on chromosomes 14 and 23 (P<0.005), respectively. In addition, 19 putative QTLs (P<0.05) accounted for 4.5–7.7% of phenotypic variance (R2) in GI, and 15 QTLs accounted for 4.2–7.3% of phenotypic variance in EGR. In lines with alleles positive for resistance contributed by both parents in combinations of two to four QTLs, dramatic reductions of >50% in both GI and EGR were observed. The transgressive segregants with epistatic effects derived from susceptible parents indicate that high levels of nematode resistance in cotton may be attained by pyramiding positive alleles using a QTL mapping approach.

Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum L. × G. barbadense L.) RIL population

“…As shown in this study and others, both superior and inferior parents may possess genetic factors that control 1 3 the performance of contrasting traits otherwise undetectable by phenotype alone (Paterson et al 1991;Tanksley and McCouch 1997;Wang et al 2012a). TM-1 alleles at the TMB1496 locus contributed to fiber tenacity (FMtQtlc05_1h) and 3-79 alleles at the TMB0400 locus contributed to lint weight (LWpQtlc21_1b) and seed weight (SWpQtlc21_1b), which is counter intuitive for these parents by phenotypic observation.…”

“…This TM-1 × 3-79 RIL population is a genetic standard resource that has been distributed by USDA-ARS among the cotton research community (Park et al 2005;Wang et al 2012a). Another major interspecific cotton RIL population used to investigate such traits is derived from a cross between Guazuncho 2 (G. hirsutum) and VH8-4602 (G. barbadense) (Lacape et al 2010).…”

“…In our present study, the parental genotypes (TM-1 and 3-79) used in making this population represent highly divergent global genetic standards for G. hirsutum and G. barbadense species, respectively, to maximize the chance of QTL identification for all these traits. Characterizing the phenotypic variation of morphological traits, yield components, and fiber quality properties facilitates the utilization of this population by other researchers who wish to further examine the co-segregation of any type of molecular markers and phenotypes (Wang et al 2012a;Said et al 2013). Obtaining the information that quantifies the phenotypic variation within the TM-1 × 3-79 RIL population allows us to determine what morphological, yield and fiber quality traits may be improved through introgression using the RIL population.…”

“…Because the parental lines of our TM-1 × 3-79 RIL mapping population represent the global genetic standards of G. hirsutum and G. barbadense, respectively, the international cotton genome research community is collaborating closely to sequence both Gossypium tetraploid reference genomes (i.e., TM-1 and 3-79). Assembly and annotation of the two parental genome sequences, along with re-sequencing of selected progeny RILs would facilitate detailed structural, functional, and evolutionary analyses of the cotton QTLs (Gao et al 2013;Lacape et al 2010Lacape et al , 2013Rong et al 2007;Said et al 2013;Ulloa et al 2013;Wang et al 2012a). More precise studies of the putative QTLs identified in this study and in many others would follow in the future when the tetraploid cotton genome sequence becomes available.…”

“…3-79 to provide better estimates of QTLs. Since its initial development and at different generations, these RILs have facilitated QTL mapping of important traits with immortal and genetically stable plant materials that were phenotyped simultaneously across multiple growth environments or geographical locations (Frelichowski et al 2006;Lacape et al 2010Lacape et al , 2013Marathi et al 2012;Park et al 2005;Wang et al 2012a). In addition, these two mapping parents (TM-1 and 3-79) are currently being sequenced to produce reference genomes for eventual analysis of all potential genes of interest in cotton (unpublished data).…”