CRYPTIC INTERSPECIFIC INTROGRESSION AND GENETIC DIFFERENTIATION WITHIN GOSSYPIUM ARIDUM (MALVACEAE) AND ITS RELATIVES

Molecular markers and cotton genetic improvement: current status and future prospects

Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands.

C, Percy R, Stewart JM. Genetic diversity and population structure of cotton (Gossypium spp.) of the New World assessed by SSR markers

A global analysis of cotton (Gossypium spp.) genetic diversity is the first step to understanding its geographical distribution, dissemination, genetic relatedness, and population structure. To assess the genetic diversity and population structure in Gossypium species, 111 cotton accessions representing five allotetraploids (AD1–AD5 genomes), 23 Asiatic diploids of the Old World (A1 and A2 genomes), and 82 diploids of the New World subgenus Houzingenia (D1–D11 genomes) species were assessed using simple sequence repeats (SSR) markers with wide genome coverage. The mean genetic distance (GD) between the two most important New World tetraploid cottons (Upland (Gossypium hirsutum L.) and Pima (Gossypium barbadense L.)) was 0.39. Among the three shrub type sections (Houzingenia, Integrifolia, and Caducibracteolata) and three arborescent sections (Erioxylum, Selera, and Austroamericana), the GD ranged between 0.19 and 0.41. Phylogenetic analyses clustered all species into distinct phylogenetic groups, which were consistent with genomic origin, evolutionary history, and geographic distribution or ecotypes of these accessions, suggesting the existence of clear structured strata. With all of the genomes, the highest statistical analysis of Structure test through measurements of ad hoc (ΔK) occurred at K = 2, with group Q1 with the Old World diploid A genomes and with group Q2 with all the New World diploids of the D genome. AD genome accessions shared nearly equal alleles from both Q1 and Q2 groups. With all of the diploids of the New World D genomes, the highest value of ΔK occurred at K = 5. These results are consistent with the fundamental knowledge of tetraploid AD-genome formation and the rapid radiation of the American diploid cotton linage that took place somewhere in southwestern Mexico, followed by a differentiation–speciation during angiosperm evolution. In addition, SSR markers provide an alternative solution for distinguishing phylogenetic relationships between accessions of different ecotypes and for elucidating population structure of cottons of the New World.