Development of EST-SSR markers related to salt tolerance and their application in genetic diversity and evolution analysis in Gossypium

Abstract

ABSTRACT. Salt stress is becoming one of the major problems in global agriculture with the onset of global warming, an increasing scarcity of fresh water, and improper land irrigation and fertilization practices, which leads to reduction of crop output and even causes crop death. To speed up the exploitation of saline land, it is a good choice to grow plants with a high level of salt tolerance and economic benefits. As the leading fiber crop grown commercially worldwide, cotton is placed in the moderately salt-tolerant group of plant species, and there is promising potential to improve salt tolerance in cultivated cotton. To facilitate the mapping of salt-tolerant quantitative trait loci in cotton so as to serve the aims of salt-tolerant molecular breeding in cotton, it is necessary to develop salt-tolerant molecular markers. The objective of this research was to develop simple sequence repeat (SSR) markers based on cotton salt-tolerant expressed sequence tags. To test the efficacy of these SSR markers, their polymorphism and cross-species transferability were evaluated, and their value was further investigated on the basis of genetic diversity and evolution analysis.

Development of EST-SSR markers related to disease resistance and their application in genetic diversity and evolution analysis in Gossypium

“…Ten of the 46 markers used in this study showed a medium level of polymorphism; 36 markers were highly polymorphic, whereas no markers showed a low level of polymorphism, thus indicating that these EST-SSR markers can provide abundant genetic information and that there was wide genetic diversity between the cotton accessions adopted in this study. The average PIC value of these disease-resistant EST-SSR markers (0.6458) were even higher than that of salt-tolerant EST-SSR markers reported in our previous study (0.4810) (Wang et al, 2014a).…”

“…Previous studies indicated that the effective amplification rate of EST-SSRs should be 60 to 90% (Saha et al, 2004), and that some primers may not be amplified once the primer covers an mRNA editing site or the amplification product contains large introns. In our previous study, the effective amplification rate was 80.3% (Wang et al, 2014a). In the current study, clear bands were amplified in 84 of the 106 NTU primer pairs, and the effective amplification rate was 79.3%, which is a high value compared to values reported in previous studies.…”

SSR-based association mapping of salt tolerance in cotton (Gossypium hirsutum L.)

“…CCRI12 and G. hirsutum L. Xinyan96-48, with 274 SSR markers, and subsequently identified 10 primer pairs that could be used to detect salt-tolerance in cotton. Wang et al (2014) developed a total of 132 pairs of non-redundant expressed sequence tag-simple sequence repeat (EST-SSR) primers related to salt-tolerance according to salt-resistant cotton ESTs and performed genetic diversity and evolution analyses on cotton. To some extent, these studies have accelerated the application of molecular markers to the breeding of salt-tolerance in cotton.…”

Intraspecific differentiation of Hancornia speciosa revealed by simple sequence repeat and random amplified polymorphic DNA markers

“…SSRs from expressed sequence tags (EST-SSRs) are markers that may be used between species belonging to different genera. The EST provides a source of polymerase chain reaction (PCR)-based markers for SSR direction (Wang et al, 2014). In the present study, we evaluated the transferability of EST-SSR markers described for Catharanthus roseus to H. speciosa.…”

“…Microsatellite markers (SSRs) have been widely used to answer questions related to population genetics (Gonzalés-Pérez et al, 2009;Madesis et al, 2014;Wang et al, 2014). However, microsatellites are expensive to use and it is time-consuming to develop specific primers for each locus of the native species (Zucchi et al, 2002).…”