**5. Association mapping for biomass traits in sorghum**

Linkage mapping and association mapping (AM) can both be used to identify QTLs by genotyping and phenotyping the segregating populations. For association mapping (AM), the population screened on the basis of phenotypic performance is subjected to molecular marker analysis, followed by the assessment of population structure and linkage disequilibrium (LD) (**Figure 4**). Linkage mapping requires few markers, due to high linkage disequilibrium (LD), but has low resolution, while association mapping needs a large number of markers to conduct a genomewide scan of a large number of diverse lines with low levels of LD. Association mapping has Genetic Improvement of Sorghum for Biomass Traits Using Genomics Approaches http://dx.doi.org/10.5772/intechopen.73010 31

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

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

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 con-

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

Linkage mapping and association mapping (AM) can both be used to identify QTLs by genotyping and phenotyping the segregating populations. For association mapping (AM), the population screened on the basis of phenotypic performance is subjected to molecular marker analysis, followed by the assessment of population structure and linkage disequilibrium (LD) (**Figure 4**). Linkage mapping requires few markers, due to high linkage disequilibrium (LD), but has low resolution, while association mapping needs a large number of markers to conduct a genomewide scan of a large number of diverse lines with low levels of LD. Association mapping has

trolling plant height, biomass, juice weight, and brix value.

**5. Association mapping for biomass traits in sorghum**

sorghum and identified two associations for height on chromosomes 6 and 9.

seed industry.

30 Advances in Biofuels and Bioenergy

located.

**Figure 4.** A simplified flow chart showing different stages of association mapping for tagging a gene of interest using germplasm accessions [36].

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 segregation.

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 242 sorghum accessions [57].

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 determine the haplotypes in sorghum.

Recently, association mapping is performed [36] for biomass-related traits in 208 sorghum accessions of Pakistan. Diversity and structure analysis as well as association mapping analysis were performed on 94 diverse accessions, which were selected through PCA of 208 sorghum accessions. About 215 alleles were detected with an average of 3.47 alleles per locus. The range of alleles varied from 2 to 5. The polymorphic SSR markers were used to identify molecular diversity, population structure, linkage disequilibrium, and marker trait associations (MTAs). Major allele frequency was ranged from 0.13 to 0.74. The average PIC value of primers was 0.51 that ranged from 0.25 to 0.62. The admixture model-based structure analysis revealed four admixture subpopulations, which indicated that all domesticated cultivars had common ancestor with continuous gene flow. The haplotype LD block analysis showed strong linkage between xtxp219 (located at 66.13 Mb) and Xcup37 (located at 61.90 Mb) with the R2 value of 1.00, which depicted that no recombinational event occurred between these two loci on chromosome 6. The markers, Xcup12 (54.22 Mb) and sb4–sb72 (41.44 Mb) were strongly linked with R2 value of 0.90. The markers within the range of R2 value 0.60–0.70 were Xcup36 (47.11 Mb), xtxp127 (44.97 Mb), xtxp045 (49.28 Mb), sb4–sb72 (41.44 Mb), SB3630 (52.81 Mb), and xtxp127 (44.97) on chromosome 6. The LD decay was estimated to be up to 10 Mb in case of chromosome 6 with R2 value of 0.440 by using 23 polymorphic SSRs. The haplotype LD block analysis of chromosome 9 showed strong linkage between SB5111 and Xcup18 with R2 value of 1.00. The pair-wise LD decay analysis revealed LD decay at 50 kb at R2 value of 0.023.

**Author details**

Pakistan

**References**

Sarmad Frogh Arshad1

Faisalabad (UAF), Pakistan

Bushra Sadia1,2\*, Faisal Saeed Awan1

, Fozia Saleem1

1 Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture,

3 Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad (UAF),

[1] Hallam A, Anderson IC, Buxton DR. Comparative economic analysis of perennial, annual, and intercrops for biomass production. Biomass and Bioenergy. 2001;**21**(6):407-424 [2] Paterson AH, Lin YR, Li Z, Schertz KF, Doebley JF, Pinson SR, Liu SC, Stansel JW, Irvine JE. Convergent domestication of cereal crops by independent mutations at corresponding

[3] Jones MB, Finnan J, Hodkinson TR. Morphological and physiological traits for higher biomass production in perennial rhizomatous grasses grown on marginal land. GCB

[4] Arshad SF, Sadia B, Awan FS, Jaskani MJ. Estimation of genetic divergence among sorghum germplasm of Pakistan through multivariate tools. IJAB. 2017;**19**:1099-1106 [5] Kamdi SR, Manjare MR, Sushir KV. Combining ability analysis of forage yield and component characters in sweet sorghum (*Sorghum bicolor* (L.) Moench). Crop Improvement.

[6] Prakash R, Ganesamurthy K, Nirmalakumari A, Nagarajan P. Combining ability for fodder yield and its components in Sorghum (*Sorghum bicolor* L). Electron Journal of Plant

[7] Mohammed MI. Potential of locally developed forage sorghum hybrids in the Sudan.

[8] Tariq AS, Akram Z, Shabbir G, Khan KS, Iqbal MS. Heterosis and combining ability studies for quantitative traits in fodder sorghum (*Sorghum bicolor* L). Journal of Agricultural

[9] Rana AS, Ahmad A, Saleem N, Nawaz A, Hussain T, Saad M. Differential response of sorghum cultivars for fodder yield and quality. Journal of Global Innovation and

and Haseeb Shaukat1

2 US-Pakistan Centre for Advanced Studies in Agriculture and Food Security

(USPCAS-AFS), University of Agriculture, Faisalabad (UAF), Pakistan

\*Address all correspondence to: bushra.sadia@uaf.edu.pk

genetic loci. Science. 1995;**269**(5231):1714-1718

Scientific Research and Essays. 2007;**2**:330-337

Agricultural Social Science. 2014;**2**:6-10

Bioenergy. 2015;**7**:375-385

2009;**36**(1):38-41

Breed. 2010;**2**:124-128

Research. 2014;**52**:329-337

, Hafeez Ahmad Sadaqat<sup>3</sup>

Genetic Improvement of Sorghum for Biomass Traits Using Genomics Approaches

,

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

33

Seven marker trait associations (MTAs) were detected by mixed linear model (MLM) approach with phenotypic variability ranging from 9.13 to 13.9% for the first year and from 6.25 to 23.05% for the second year. Four MTAs were associated with plant height, days to 50% flowering, and leaf length on chromosome 6 and three on chromosome 9 with the same traits. A total of five SSR markers expressed significant MTAs; three of these (Xgap072, Xtxp265, and SB3789) were associated with plant height, days to 50% flowering, and leaf length traits on chromosome 6. Two markers Xtxp283 and SB5040 were associated with plant height, leaf length, and days to 50% flowering on chromosome 9. Hence, chromosomes 6 and 9 appeared to carry important QTLs for biomass-related traits in sorghum.
