Abstract
BackgroundJute (Corchorus spp.) is the most important natural fiber crop after cotton in terms of cultivation area and production. Salt stress greatly restricts plant development and growth. A high-density genetic linkage map is the basis of quantitative trait locus (QTLs) mapping. Several high-density genetic maps and QTLs mapping related to salt tolerance have been developed through next-generation sequencing in many crop species. However, such studies are rare for jute. Only several low-density genetic maps have been constructed and no salt tolerance-related QTL has been mapped in jute to date.ResultsWe developed a high-density genetic map with 4839 single nucleotide polymorphism markers spanning 1375.41 cM and an average distance of 0.28 cM between adjacent markers on seven linkage groups (LGs) using an F2 jute population, LGs ranged from LG2 with 299 markers spanning 113.66 cM to LG7 with 1542 markers spanning 350.18 cM. In addition, 99.57% of gaps between adjacent markers were less than 5 cM. Three obvious and 13 minor QTLs involved in salt tolerance were identified on four LGs explaining 0.58–19.61% of the phenotypic variance. The interval length of QTL mapping varied from 1.3 to 20.2 cM. The major QTL, qJST-1, was detected under two salt stress conditions that explained 11.81 and 19.61% of the phenotypic variation, respectively, and peaked at 19.3 cM on LG4.ConclusionsWe developed the first high-density and the most complete genetic map of jute to date using a genotyping-by-sequencing approach. The first QTL mapping related to salt tolerance was also carried out in jute. These results should provide useful resources for marker-assisted selection and transgenic breeding for salt tolerance at the germination stage in jute.
Highlights
Jute (Corchorus spp.) is the most important natural fiber crop after cotton in terms of cultivation area and production
We identified major and minor Quantitative trait locus (QTL) involved in salt tolerance, and determined the phenotypic variance
We identified three obvious QTLs with over 3.5 logarithm of odds (LOD) values on LG4 under the two salt stress conditions, and a major QTL was detected under the two conditions simultaneously, designated qJST-1 (Table 2; Fig. 3)
Summary
Jute (Corchorus spp.) is the most important natural fiber crop after cotton in terms of cultivation area and production. Several high-density genetic maps and QTLs mapping related to salt tolerance have been developed through next-generation sequencing in many crop species. Jute is a diploid (2n = 14) Malvaceae herb plant that includes 50–60 species [1] It is the most important and used natural fiber crop in the world after cotton in both the cultivation area and production [2]. 20% of all irrigated lands are affected by salinity [12], which is expected to become more serious and expansive in the face of global climate change and environmental pollution [13] Salt stress causes both primary and secondary effects in a plant. Understanding the genetic mechanisms underlying plant salt tolerance and mapping quantitative trait loci (QTLs) related to salt tolerance are crucial for improving the salt tolerance of economically important plants
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