**3. Second-generation sequencing resources for yield improvement in wheat**

Researchers have focused on discovering SNPs to be used as genetic markers, because they have many advantages. SNPs act as codominant, single-locus, biallelic markers offering a lower error rate, and higher accuracy than SSR markers. However, the nature of polyploidy and having similar sequences among the A, B, and D genomes makes it difficult to identify SNPs [100]. Therefore, progress in SNP detection has been limited, especially related to yield and its related traits. With the advancement in next-generation sequencing (NGS), sequencing has become increasingly popular due to the rapid development of NGS technologies, including SOLiD/Ion Torrent PGM from Life Science, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and 454 FLX Titanium/GS Junior by Roche [101]. These technologies have led to the implementation of high-density SNP genotyping in wheat [99, 102].

An important milestone in wheat genomic research was accomplished in 2012 with the completion of *de novo* sequencing of bread wheat, the variety Chinese Spring (CS42), facilitating advances in genomic research into the genus *Triticum* and providing insights into the polyploidization and domestication of wheat. Brenchley et al. sequenced the wheat genome using Roche 454 pyro-sequencing technology (GS FLX Titanium and GS FLX+ Platforms [11]. To identify the three component genomes (A, B, and D) of hexaploid wheat, the following technologies have been applied: Illumina sequence assemblies of *Triticum monococcum* (related to the A-genome donor), *Ae. speltoides* complementary DNA assemblies, and 454 sequences from *Ae. tauschii* (the D-genome donor). Sequence analysis revealed that the A, B, and D genomes have estimated to consist of approximately 28,000, 38,000, and 36,000 genes, respectively. As a consequence, they identified the number of genes in wheat to be between 94,000 and 96,000. Like *G. hirsutum* [103] and soybean [104], wheat also has experienced a recent whole genome duplication (WGD) at 0.5 MYA and about 3.5 MYA. Brenchley et al. also examined gene conservation between wheat and its most closely related species *Brachypodium distachyon* and detected a high degree of conservation between the two species [11]. A large set of SNPs (132,000 SNPs) in A, B, and D genes will enhance future studies aimed at identifying QTLs and discovering associations of traits.

*Xbarc147* spanning a region of approximately 20 cm on chromosome 3BS. Additional SSR markers have been reported for strip rust resistance genes, including the *Xgwm501* marker linked to *Yr5* [92], and the *Xpsp3000* marker linked to *Yr10* [93]. A microsatellite linkage map of the powdery mildew resistance gene *Pm5e* on chromosome 7B has constructed with 20 microsatellite loci, consisting of two codominant markers *Xgwm783* and *Wgwm1267* located close to *Pm5e* with a linkage distance of 11.0 cm and 6.6 cm, respectively [94]. The detection of QTL linked to FHB resistance has found that two microsatellite loci, *Xgwm533* and *Xgwm*, were significantly associated with QTL for FHB [95]. In 2004, a SSR-based consensus map has been completed by Somers et al. [96] that has been widely used a reference. Furthermore, five QTLs, *QYld.crc-1A, QYld.crc-2D, QYld.crc-3B, QYld.crc-5A.1*, and *QYld.crc-5A.2*, controlling grain yield have been identified on chromosomes 1A, 2D, 3B, and 5A [97]. Other QTLs associated with 1000 grain weight, spikes meter−2, seed number spike−1, average seed weight spike−1, harvest index, days to heading, days to maturity, and grain filling time have also been detected in the Superb/BW278 mapping population. Liu et al. [98] performed association mapping by genotyping wheat germplasm accession from China using SSR markers and EST-SSR markers, detecting 10 SSR markers on chromosome 4A associated with plant height, spike length, spikelets per spike, spikelet density, grains per spike and thousand-kernel weight. Even though studies involving RFLP, RAPD, and AFLP markers have only been used for identification and mapping of QTLs and genes, they are less likely to be applied into breeding programs because the application of these markers is likely to be less efficient for

**3. Second-generation sequencing resources for yield improvement** 

implementation of high-density SNP genotyping in wheat [99, 102].

Researchers have focused on discovering SNPs to be used as genetic markers, because they have many advantages. SNPs act as codominant, single-locus, biallelic markers offering a lower error rate, and higher accuracy than SSR markers. However, the nature of polyploidy and having similar sequences among the A, B, and D genomes makes it difficult to identify SNPs [100]. Therefore, progress in SNP detection has been limited, especially related to yield and its related traits. With the advancement in next-generation sequencing (NGS), sequencing has become increasingly popular due to the rapid development of NGS technologies, including SOLiD/Ion Torrent PGM from Life Science, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and 454 FLX Titanium/GS Junior by Roche [101]. These technologies have led to the

An important milestone in wheat genomic research was accomplished in 2012 with the completion of *de novo* sequencing of bread wheat, the variety Chinese Spring (CS42), facilitating advances in genomic research into the genus *Triticum* and providing insights into the polyploidization and domestication of wheat. Brenchley et al. sequenced the wheat genome using Roche 454 pyro-sequencing technology (GS FLX Titanium and GS FLX+ Platforms [11]. To identify the three component genomes (A, B, and D) of hexaploid wheat, the following technologies have been applied: Illumina sequence assemblies of *Triticum monococcum* (related

MAS [99].

24 Wheat Improvement, Management and Utilization

**in wheat**

Since the completion of the draft sequence of wheat, extensive efforts have put into the identification of various molecular markers influencing yield to increase MAS efficiency. Based on the genotype by sequencing (GBS) approach, the linkage map of wheat comprised of markers including 538 GBS Bin, 258 AFLPs, 175 SSRs, and an EST has been constructed in 2014 [105]. They identified five QTL regions linked to thylakoid membrane damage (TMD), SPAD chlorophyll content (SCC), and plasma membrane damage (PMD), known as indicatives of high temperature tolerance, on chromosomes 6A, 7A, 1B, 2B and 1D and also detected some of the SSR markers associated with these traits such as the SSR marker *Xbarc121* and *Xbarc49* for all three traits and *gwm18* and *Xbarc113* for SCC. More SNP and SSR markers have been investigated using the 9 K Infinium iSelect Beadchips [106]. The SNP distribution between cultivars and landraces has provided impacts on our understanding of crop improvement on the structure of genetic diversity and insight into signatures of selection. Liu et al. reported six SNPs from two genes, *wsnp\_CAP11\_c209\_198467* and *wsnp\_JD\_c4438\_5568170*, showed significant association with soil-borne wheat mosaic virus (SBWMV) resistant which can be used in MAS to improve SBWMV resistance in wheat breeding [107]. Using the high-density Illumina iSelect 90K SNP assay, a linkage map spanning 3609.4 cm was constructed based on 5636 polymorphic SNP markers, with an average length of 171.9 cm per chromosome and marker density of 0.64 cm [108]. Association of agronomic traits with 1,366 SNP markers in durum wheat has been performed by Hu et al. [109]. By genotyping 150 accessions of durum wheat germplasm based on the Illumina Bead Array platform and Golden Gate Assay, a large amount of SNP markers were detected associated with key yield-related traits including plant height, number of effective spikes, length of main spike, number of spikelets per plant, panicle neck length of main spike, grain number per plant, grain weight per plant, and 1000-grain weight. These SNP markers have enhanced the previous QTL analyses and can be utilized for MAS to improve yield in wheat.
