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The genus Gossypium is comprised of 50 diverse cotton species representing eight different genomes (A through G and K), however, phylogenetic relationship using various DNA marker types such as RAPD and SSRs was determined on limited number of cotton species. In this report, we have demonstrated the application of genomic SSRs (gSSRs) and EST-SSRs, and after combining both the data sets, for resolving the phylogenies of 36 cotton species including seven races. Out of the 100 primer pairs surveyed (50 for gSSRs and 50 for EST-SSRs), 75 produced scorable amplification products in all species. Out of these, 73 were found to be polymorphic and amplified 135 alleles ranging from 1 to 5 alleles per SSR marker (average 2.87 alleles per marker). The gSSRs amplified higher number of alleles (72) compared to the EST-SSRs (63). In total 22 highly informative SSRs with PIC values ≥0.5 were identified. Genomic SSRs containing di-while EST-SSRs containing tri-nucleotide repeats exhibited high polymorphism compared to the other nucleotide repeats containing gSSRs/EST-SSRs. Number of tandem repeats and polymorphism were positively correlated. Neither the type of chromosome nor the location of the SSRs showed association with the polymorphism. Gossypium herbaceum var. africanum (Watt) Hutch. ex and Ghose and Gossypium robinsonii F. Muell. were found the most genetically diverse, while among races of Gossypium hirsutum L. “yucatanense” and G. hirsutum “punctatum” were found genetically diverse. Of the three data sets, clustering analysis based on EST-SSRs and combined data sets, revealed parallel results reported in earlier studies. This study further confirmed that Gossypium darwinii Watt has close relationship with Gossypium barbadense L. Moreover, Gossypium raimondii Ulbr. and G. herbaceum/Gossypium arboreum L. are close living relatives of the ancestor allotetraploid species. Our studies suggest that for resolving phylogenetic relationship among the various plant species EST-SSRs could be a better choice. This information can be instrumental in transferring novel alleles or loci from the wild species into the cultivated cotton species which would set a stage for cultivating genetically diverse cultivars—a way to achieve sustainable cotton production in changing climate.

The sustainable production of the soybean (Glycine max L. Merr.) is at stake due to increased salinization, frequent drought periods, flooding, unusual fluctuations in temperature, and rainfall pattern and frequency. The negative consequences of the changing climate are further complicating the situation. Conventionally, different traits such as root length, photosynthetic rate, seed size, etc. have been used as selection criteria for selecting resilient genotypes. Since 1995, DNA markers associated with different traits have been used for selecting the genotypes with excellent genetics; however, complex traits like tolerance to different abiotic stresses need further investigation to identify QTLs, which can be used confidently in initiating marker-assisted breeding in soybeans. A number of studies explored the various adaptation mechanisms at the molecular level, which help soybean plants to counter the abiotic stresses. For example, a number of transcription factors (TFs) including DREBs, ERFs, ZIP, WRKY, and MYB have been identified in soybeans. In another study, the role of the HD-Zip gene family in conferring drought and saline environments was described in soybeans. Similarly, a total of 61 HSP70 genes located unevenly on 17 different chromosomes were identified, which have a role in imparting tolerance to heat stress. Reports for transferring the genes and or TFs involved in conferring tolerance to abiotic stresses in soybeans are scanty. A P5CR gene, DREB1DTF, and the NTR1 gene were introduced in soybeans, which showed improved tolerance to drought. The expression of an Arabidopsis vacuolar Na+/H+antiporter gene (AtNHX1) in soybeans demonstrated improved tolerance to salt. Overexpression of a Solanumtorvum Δ1-pyrroline-5-carboxylate synthetase gene (StP5CS) in soybeans resulted in a higher level of salt tolerance. In the future, utilization of untapped genetic diversity available in the wild germplasm accessions, understanding genetic mechanisms using TILLING approach, identification of new DNA markers using next-gen sequencing tools, precise editing of the soybean genome using new editing tools like ZFNs and CRISPR-Cas9, and exploitation of the chloroplast-based transformation approach would be the ultimate choice for improving genetics of soybeans for mitigating the abiotic stresses.

Revealing the genetic underpinnings of cotton productivity will require understanding both the prehistoric evolution of spinnable fibers, and the results of independent domestication processes in both the Old and New Worlds. Progress toward a reference sequence for the smallest Gossypium genome is a logical stepping-stone toward revealing diversity in the remaining seven genomes (A, B, C, E, F, G, K) that permitted Gossypium species to adapt to a wide range of ecosystems in warmer arid regions of the world, and toward identifying the emergent properties that account for the superior productivity and quality of tetraploid cottons. The greatest challenge facing the cotton community is not genome sequencing per se but the conversion of sequence to knowledge.

Knowledge about the extent of genetic diversity/relatedness in mango germplasm is vital for developing coherent strategies for future gains in productivity. The genetic diversity/relatedness among mango cultivars/genotypes developed in Pakistan has not been investigated previously. We have assessed the genetic diversity among 25 mango genotypes/cultivars using randomly amplified polymorphic DNA (RAPD). Sixty random ten-mer primers were surveyed, out of which 45 yielded amplicons in all the genotypes. Genetic similarity between genotypes/cultivars was in the range of 64–89% with an average of 74%. Similarly, the genetic relatedness among all variants derived from a mango cultivar Chaunsa was in the range of 81.18–88.63%. These coefficients were utilized to construct a dendrogram using the unweighted pair group of arithmetic means (UPGMA). The genotypes were grouped into three (A, B, C) clusters. Generally, genotypes originating from Pakistan were grouped in cluster ‘A’ while cluster ‘B’ primarily composed of southern India as well as Florida cultivars. Kensington Pride was the most distantly related genotype which grouped with Maya and Yakta, forming a distinct cluster ‘C’.

Genetic diversity is an area of concern for sustaining crop yield. Information on genetic relatedness/diversity among Gossypium arboreum L. cultivars/genotypes is scanty. We have used random amplified polymorphic DNA (RAPD) analysis to assess the genetic divergence/relationship among 30 genotypes/cultivars of G. arboreum. Of 45 primers surveyed, 63% were polymorphic. Out of the total number of loci amplified, 36% were polymorphic. The calculated genetic similarity between the cultivars/genotypes was in the range of 47.05–98.73%. Two genotypes, HK-244 and Entry-17, were the most distantly related. The average genetic relatedness among all the genotypes was 80.46%. However, most of the cultivated varieties showed a close genetic relationship, indicating a narrow genetic base in comparison to the non-cultivated germplasm. The calculated coefficients were used to construct a dendrogram using the unweighted pair group of arithmetic means (UPGMA) algorithm, which grouped the genotypes/cultivars into two major and three smaller clusters. The study is the first comprehensive analysis of the genetic diversity of G. arboreum germplasm and identifies cultivars that will be useful in extending the genetic diversity of cultivated varieties and future genome mapping projects.

Mango Malformation (MM) disease is a major constraint to mango production. A total of 20 Fusarium isolates from MM-affected mango plants were collected from 14 locations in Pakistan and assessed for genetic diversity using the random amplified polymorphic DNA (RAPD) technique. A total of 393 fragments were amplified after screening with 50 random primers. The amplifications with 45 primers identified scoreable polymorphisms among the isolates. A genetic similarity matrix based on Nei and Li’s index determined coefficients ranging from 46.46% to 92.51%. These coefficients were used to construct a dendrogram using the UPGMA algorithm. The isolates grouped into two main clusters, comprising 13 and 7 isolates respectively, at a genetic relatedness of 52%. Within the clusters, Fusarium isolates were not necessarily related either by geographic origin or by the mango cultivar from which they were isolated. RAPD proved a reproducible and tractable means of differentiating Fusarium isolates. These findings also suggest that some infections originate not from adjacent plants within an orchard but from geographically distant areas; indicating that most probably infection occurs in nurseries prior to plants being transported around the country for subsequent cultivation, and that improved plant hygiene could significantly curb MM infection and spread.

Epidemics of cotton leaf curl virus disease (CLCD) was the compelling factor in the decision to devise new strategies for cotton breeding programs of Pakistan. The genetic similarity among the elite cotton (Gossypium spp.) cultivars released before the advent of CLCD epidemics was in the range of 81.5 to 93.41%. New cultivars were developed by crossing the exotic resistant germplasm (LRA-5166, CP-15/2, and Cedix) with adapted varieties highly susceptible to CLCD. A study was designed to assess the genetic relatedness or diversity among the newly released, extremely resistant and resistant cultivars. After screening 27 cotton genotypes by different diagnostic methods such as field evaluation, whitefly-transmission studies, grafting, dot-blot hybridization, and multiplex PCR using conserved primers sequences, 20 extremely resistant and resistant cultivars were selected for a random amplified polymorphic DNA (RAPD) analysis. The genetic similarity of the exotic germplasm with the elite cultivars was in the range of 81.45 to 90.59%. Similarly, the genetic relatedness among the elite cultivars was in the range of 81.58 to 94.90%. The average genetic similarity among all studied genotypes was 89.55%. We have demonstrated that only cultivar VH-137 possesses a diverse genetic background. Our study suggests the need to breed for high genetic diversity to serve as a buffer against potential epidemics.

Numerous genomic tools have been used vigorously for studying the inherent genetic polymorphisms which were instrumental in resolving the phylogenies of many crop species, developing genetic maps, initiating marker assisted selection and incorporating genes from distantly related taxa-introduction of Bt genes in cotton, corn etc., these together set a stage for developing crop varieties with improved genetic potential to multiple stresses. Wider adaptation of genomic based breeding in crop improvement programs is impeded due to the narrow genetic base resulting from selection pressures applied during the domestication of many plant taxa, which also can confer genetic vulnerability to crop gene pools. Genomic based breeding may contribute to increasing crop genetic diversity by introgressing novel alleles from feral and or alien species. Association mapping approaches coupled with identifying single nucleotide polymorphisms the most elemental form of polymorphism in the genomes, may facilitate breeding by design. In this article, efforts to advance genomic-based breeding for improving crop species, providing food, feed, fuel and fiber to the world community, will be discussed.

Since 6000 BC, cotton has been cultivated for lint fiber, which now dominates the natural textile industry worldwide. Common resources such as an integrated web database, a microsatellite database, and comparative quantitative trait loci (QTL) resources for Gossypium have accelerated the progress towards quantifying the impact of repeated human dispersals and selection regimes on various gene pools of the genus Gossypium. Out of 50 Gossypium species, four have been domesticated—two diploids and two tetraploids—for elimination of hard seed coat, improvement in lint percentage of about 40% and fiber length of 22%, larger boll size, and day-neutral reproductive habit. The major drawback of domestication is the lack of genetic diversity. This lack of genetic diversity is observed more in Gossypium hirsutum L. cultivars characterizing upland cotton than in Gossypium barbadense, typical of Pima and Egyptian cotton. Much of the genetic diversity among G. barbadense cultivars is attributed to the introgression of G. hirsutum alleles. This process highlights the importance of introgression of new alleles from accessions of all the Gossypium species into cultivated cotton species. Among the genomic resources, about 16,162 publicly available SSRs and 312 mapped cotton RFLP sequences containing simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), and random amplified polymorphic DNA (RAPD) markers have been surveyed on numerous mapping populations, and developed about 26 linkage maps (SSR, RFLP, AFLP, and RAPD). Reports show the identification of DNA markers associated with over 29 important traits or QTLs such as fiber quality and yield, leaf and flower morphology, trichome density and their distribution, and disease resistance. In comparative mapping studies, 432 QTLs mapped on 11 different mapping populations were aligned on a high-density reference map containing 3,475 loci. In a meta-analysis study of over 1,000 QTLs obtained from backcross population and recombinant inbred line populations derived from the same parents, most consistent meta-clusters were reported for fiber color, fineness, and length. For exploring the function of genes, the targeting induced local lesions in genomes (TILLING) approach—avoiding gene transfer process was used for identifying a brassino steroid receptor gene that is involved in fiber development. Lastly, cotton genome has been enriched with genes isolated from distantly related organisms using various transformation methods. For example, Cry1Ac, Cry1Ab, and herbicide-resistant genes were transformed in cotton that covered a vast majority of cotton acreage worldwide. Here the authors discuss investigations for improving the efficacy of transformation and regeneration systems, and for searching new genes or silencing the unwanted cotton genes using RNAi technology. We suggest initiating projects on sequencing the diploid and tetraploid genomes for exploring the extent of genetic variations, developing TILLING populations, initiating nested association mapping studies, and developing third generation genetically modified cotton, collectively setting the stage for sustaining cotton production under continually changing production conditions, climates, and human needs.