**4. QTL mapping of quantitative traits in sorghum**

Germplasm characterization using morphological traits has some limitations. The expression of a phenotype is mostly influenced by the environment and depends upon plant organ as well as plant developmental stages. Owing to these shortcomings, it is the least preferred means of characterizing crop germplasms. Hence, investigating DNA polymorphism is a reliable means of genetic diversity assessment. Molecular markers are extensively used in molecular breeding being reliable, abundant, phenotypically unbiased, and time and stage independent. These markers are helpful in improving breeding programs through different ways. The marker-assisted selection (MAS) technology makes use of an association between the expression of desired characters and markers present in the DNA. Quantitative trait loci (QTL) for many traits can be evaluated by using molecular markers [38]. For a given trait in a particular population, increasing marker density can increase the resolution of the genetic map, thus enhancing the precision of QTL mapping. Genetic mapping studies are based mainly on BTx623 and other grain sorghum types. Widely used polymerase chain reaction (PCR)-based markers are RAPD (random amplified polymorphic DNA), AFLP (amplified fragment length polymorphism), SSRs (simple sequence repeats), STS (sequence-tagged sites), and DArTs (diversity arrays technology) [39–41].

Recently, there has been a growing interest in exploiting QTL mapping for different traits. About >700 QTLs have been identified for several traits in sorghum (http://www.gramene. org). However, fewer studies have been carried out to find out the molecular basis of these traits.

The biomass trait of sorghum depends on stem height and thickness, which are vital for bioethanol production. Taller varieties produce higher biomass with thicker stem and higher sugar contents. Height is positively correlated with biomass production and independent of stem structural composition like cellulose, hemicellulose, and lignin content. The QTL for total dry biomass has been found to localize with height QTLs [42, 43]. In sorghum, height is controlled by few QTLs. Genetic study has identified four loci controlling stem height: *Dw1*, *Dw2*, *Dw3*, and *Dw4* [44]. *Dw3*, which encodes a P-glycoprotein that controls polar auxin transport, has been cloned [45]. This gene is also co-localized with a height QTL on chromosome 7 [42]

**Figure 2.** Biplot with cumulative sorghum variables and genotypes.

**Figure 1.** Biplot with sorghum genotypes.

28 Advances in Biofuels and Bioenergy

UPGMA analysis generated 9 morphotypes of 24 sorghum genotypes (**Figure 3**). Total of 24 genotypes were divided into five different classes. Cluster analysis revealed that the main cluster was divided into two major clusters. The first subcluster comprised four genotypes (6, 24, 16, and 20), while the second subcluster was further subdivided into four different small clusters. Two genotypes were present in the cluster with blue-colored cluster, and 11 genotypes were placed in light blue-colored cluster. The class represented by red color consists of two genotypes, whereas the class represented by green color includes three genotypes.

and *Dw2* with QTL on chromosome 6 [46]. Another QTL on chromosome 9 was also found for height [42]. Using 377 sorghum accessions and 49 SSR markers, a height QTL (Sb-HT9.1) was mapped. Likewise, Murray et al. [43] used 47 SSR and 322 SNP markers on 125 genotypes of sorghum and identified two associations for height on chromosomes 6 and 9.

Maturity (days to 50% flowering) is also positively correlated with the biomass production [47]. The photoperiod sensitivity in sorghum was initially reported to be controlled by single maturity locus Ma1 [48]. Any genotype with a dominant Ma1 allele will show a photoperiod response, while the homozygous recessive (Ma1) will flower early. Ma1 was cloned and reported as pseudo-response regulator protein 37 [49]. The first maturity cloned locus in sorghum was Ma3 that encoded a phytochrome B [50]. Genotypes with total loss of functional ma3R allele of Ma3 are insensitive to photoperiod and flower early regardless of Ma1 allele and day length. There is an epistatic interaction between Ma1 and Ma3. Few more maturity loci have also been reported in sorghum, e.g., Ma2, Ma4, Ma5, and Ma6, with very little information about their functions. Ma2 is unmapped and shows interaction with Ma1 [51], while Ma4 is thought to be on chromosome 10 [26]. For the production of photosensitive hybrids from two plants, the Ma5-Ma6 interaction has been extensively used by the biomass sorghum seed industry.

Murray et al. [52] identified one QTL for brix (located on chromosome 1) by using 47 SSRs and 322 SNPs for a diverse panel of 125 sweet sorghums. Six marker loci related to plant height and 10 loci to plant maturity were identified [53] by using 14,730 SNPs for sorghum mini core collection. Once identified, QTLs need validation/confirmation in varying experimental conditions prior to exploitation for MAS. Wang et al. [54] used 181 recombinant inbred lines (Shihong137, a dwarf grain sorghum, x L-Tian, a tall sweet sorghum) to validate QTLs controlling plant height, biomass, juice weight, and brix value.

The study identified seven QTLs for biomass-related traits including plant height, juice, and stem fresh weight under four different environmental conditions, while three of these seven QTLs were under strong epistasis. Co-localization of many biomass-related QTLs with previously reported height QTLs confirmed that plant height regulates biomass in sorghum. On the other hand, few QTLs, namely, qSFW1–qSFW2, qSLFW6–qSLFW1, and qSLFW6–qSLFW2, were mapped to chromosomal positions where no height QTLs were located.

the ability to evaluate multiple haplotypes. Moreover, association analysis is an efficient strategy to genetically dissect the complex traits that deviate from classical Mendelian pattern of

**Figure 4.** A simplified flow chart showing different stages of association mapping for tagging a gene of interest using

Genetic Improvement of Sorghum for Biomass Traits Using Genomics Approaches

http://dx.doi.org/10.5772/intechopen.73010

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Though originally designed for human genetics, exploitation of association mapping is picking momentum in plant improvement. In sorghum, association mapping is being applied for its genetic enhancement by phenotypic evaluation of sorghum germplasm, identifying and mapping QTLs associated with desired traits and selecting the genotypes (parents) that carry favorable alleles for gene introgression through MAS. Using 107 representative sorghum accessions and 98 SSR markers, Shehzad et al. [55] reported the association of 14 SSR loci with four traits including days to heading, days to flowering, number of panicles, and panicle length in sorghum. Another report identified two SSR markers consistently associated with plant height under two different environments [56]. Plant height and maturity date were also reported to be associated with 5 out of 39 SSR markers on chromosomes 6, 9, and 10 in

About 300 diverse accessions of sorghum were evaluated [58] to conduct association analysis of seedling phenotypic variation during cold and heat stress treatments. They identified and validated 30 and 12 SNPs associated with cold and thermal tolerance, respectively, to deter-

segregation.

germplasm accessions [36].

242 sorghum accessions [57].

mine the haplotypes in sorghum.
