Mapping QTLs for traits related to phenology, morphology and yield components in an inter-specific Gossypium hirsutum×G. barbadense cotton RIL population

Abstract

Two major cultivated cotton species, Gossypium hirsutum (Gh) and G. barbadense (Gb) contribute to the bulk of cotton fiber production worldwide (95%). These species are largely inter-fertile and each displays a series of distinctive characteristics in terms of numerous botanical features and, more importantly, in their agronomic performance, adaptability and overall fiber quality. A recombinant inbred line (RIL) population derived from an inter-specific cross between Gh and Gb, used previously for QTL mapping of fiber quality characteristics, has also been evaluated over 6 sites and 2 years for various plant morphological, phenological and yield component traits. A total of 27 traits were assessed across a varying number of locations (up to 6 locations, in Australia, USA, Brazil, Cameroon, Belgium and France) and years, representing up to 10 different combinations. Variability in many of these traits was observed among the RILs and they frequently showed transgression. One hundred and sixty six significant QTLs, covering the 27 traits, were detected by composite interval mapping when using individual datasets. Cases of confirmation of localizations of individual QTLs from different data sets were detected in 27 instances, indicating that the 166 individual QTLs in this study could be represented by a maximum of 121 chromosome positions. QTL were shared between traits related to hairiness (22 individual QTLs), plant morphology of vegetative (29 QTLs) and reproductive (37 QTLs) parts, phenology (17 QTLs), and yield-related traits (61 QTLs). This is the first report of QTL mapping in cotton for various within-boll yield-related traits assessed on a per-seed basis, including fiber mass per unit of seed surface area (5 QTLs), calculated number of fibers per seed (2 QTLs) or per unit of seed surface area (1 QTL). This report confirms the importance of considering such basic yield components in selection for better yielding cotton varieties.

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

“…Understanding the underlying genetic control of biological processes for favorable traits is relevant to a range of research objectives. Such understanding has potential applications for cotton crop improvement Cao et al 2014;Lacape et al 2013;Ning et al 2014;Rong et al 2007;Ulloa et al 2005Ulloa et al , 2013.…”

“…To date, several thousands of SSR and SNP markers have been developed in cotton (Blenda et al 2012;Fang and Yu 2012;Guo et al 2007;Lacape et al 2009;Yu et al 2012a) and they have been surveyed for polymorphism against a 12-genotype germplasm standard (diversity panel) of six Gossypium species ). The localization of SSR and SNP markers to all 26 chromosomes and the creation of highdensity genetic maps for the tetraploid cotton genome provide opportunities to identify genetic factors controlling and regulating the expression of traits of interest (Lacape et al 2013;Li et al 2013;Marathi et al 2012;Zhu et al 2011). However, due to the allopolyploid nature of the cotton genome, certain chromosomal structures remain to be resolved.…”

“…Most traits of interest in crop plants are likely the product of complex biological processes in which multiple genes and environments interact to quantitatively determine phenotypic expression Collard and Mackill 2008;Huang et al 2012;Lacape et al 2010Lacape et al , 2013Paran and Zamir 2003;Paterson et al 1988Paterson et al , 1991Rong et al 2007). A quantitative trait locus (QTL) mapping approach can be informative for studying quantitative inheritance, for detecting genomic regions associated with morphological, yield and fiber quality traits, and for identifying molecular markers linked to the genes conferring the phenotypic expression of the important traits (Draye et al 2005;Kohel et al 2001;Lacape et al 2005;Luan et al 2009;Park et al 2005;Shen et al 2005;Song and Zhang 2009;Ulloa et al 2007;Zhu et al 2011).…”

Modifications to aLATE MERISTEM IDENTITY1gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutumL.)

“…The L-D 1 locus was placed on the short arm of chromosome 15-D 1 (Chr15) using cytogenetics (26,27) and confirmed by quantitative trait loci (QTL) mapping (28)(29)(30). The L-D 1 locus was localized to a 5.4 cM interval near the telomere of Chr15 (31), and shuttle mapping using the laciniate gene (L-A 2 L ) from G. arboreum further reduced the candidate region to 112 kb and 10 genes (22).…”

Australian Cotton Germplasm Resources

“…The two parents; Guazuncho 2 (G. hirsutum), and VH8-4602 (G. barbadense), were chosen for their agronomic performance (Guazuncho 2) and superior fibre quality parameters (VH8-4602) [53]. This population was grown in several countries including Australia in the glasshouse and field and analysed for many different traits (including fibre, leaf shape hairiness, boll size and number and earliness) and genotypes consisting of 1,745 loci derived from 597 SSR and 763 ALFP markers [54][55][56]. Not all of the lines performed well under Australian conditions with only about 55 flowering within an acceptable timeframe for harvesting and thus seed stocks are severely restricted for most of the RILs.…”