A Genome-Wide Association Study of Wheat Spike Related Traits in China

Abstract

Rapid detection of allelic variation and identification of advantage haplotypes responsible for spike related traits play a crucial role in wheat yield improvement. The released genome sequence of hexaploid wheat (Chinese Spring) provides an extraordinary opportunity for rapid detection of natural variation and promotes breeding application. Here, selection signals detection and genome-wide association study (GWAS) were conducted for spike related traits. Based on the genotyping results by 90K SNP chip, 192 common wheat samples from southwest China were analyzed. One hundred and forty-six selective windows and one hundred and eighty-four significant SNPs (51 for spike length, 28 for kernels per spike, 39 for spikelet number, 30 for thousand kernel weight, and 36 for spike number per plant) were detected. Furthermore, tightly linkage and environmental stability window clusters and SNP clusters were also obtained. As a result, four SNP clusters associated with spike length were detected on chromosome 2A, 2B, 2D, and 6A. Two SNP clusters correlated to kernels per spike were detected on 2A and 2B. One pleiotropy SNP cluster correlated to spikelet number and kernels per spike was detected on 7B. According to the genome sequence, these SNP clusters and their overlapped/flanking QTLs which have been reported previously were integrated to a physical map. The candidate genes responsible for spike length, kernels per spike and spikelet number were predicted. Based on the genotypes of cultivars in south China, two advantage haplotypes associated with spike length and one advantage haplotype associated with kernels per spike/spikelet number were detected which have not been effectively transited into cultivars. According to these haplotypes, KASP markers were developed and diagnosed across landraces and cultivars which were selected from south and north China. Consequently, KASP assay, consistent with the GWAS results, provides reliable haplotypes for MAS in wheat yield improvement.

Genome-wide association study reveals new loci for yield-related traits in Sichuan wheat germplasm under stripe rust stress

“…In other words, SlPS, TKW and SlC were more stable than FTN and KPSl. Consistent with many other reports, FTN had a low heritability and was strongly influenced by environments [5,9,31] and KPSl also displayed relatively low heritability, whereas SlPS, TKW and SlC had relatively higher heritabilities [3,9,[32][33][34].…”

Genome-wide and SNP network analyses reveal genetic control of spikelet sterility and yield-related traits in wheat

“…The positive relationships between FSS (or FSS%), GNFS with BY, TKW, HI, SPS and GN that found in the current study, indicate that improving grain yield through enhancing spikelet fertility together with TKW, SPS and BY is plausible. It might be attributed to the genetic material (ancient cultivars) used in the current study which are carrying allele(s) that not present, or present at low frequency in breeding lines or elite/modern cultivars used in the previous studies 8, 24,25 . The elite/ modern cultivars were selected for a specific purpose based on origin 8 , and always characterized with low number of kernels per spikelet, and less resistance/tolerance to biotic/abiotic stresses compared with old cultivars 26 .…”

“…The newly added spikelet related-traits in this study demonstrated the importance of studying such traits which showed high natural variation. The natural variation of spikelet fertility/sterility traits and grain-yield-related traits has been recently explored in wheat 8,24 .…”

“…It has been shown that a negative correlation between TKW with SPS and GN in Chinese wheat 24 might be a consequence of trade-offs between GN and TKW with BY and HI. Such negative correlation restricts the grain yield and genetic gains of these traits 25 , or a competition for assimilates between spikelets that leads to unbalanced distribution of GN within FSS and florets along the spike 8 .…”

TaAPO-A1, an ortholog of riceABERRANT PANICLE ORGANIZATION 1, is associated with total spikelet number per spike in elite hexaploid winter wheat varieties (Triticum aestivumL.)

“…In the recent past, several genes controlling spike morphology have been investigated and described in temperate cereals (Gauley and Boden 2019; Koppolu and Schnurbusch 2019). From a plant breeder’s viewpoint, most spike morphological traits in wheat such as spike length and spikelet number behave as quantitative traits, and various QTL and association studies have recently been published (Deng et al 2017; Guo et al 2017; Liu et al 2018; Sakuma et al 2019; Würschum et al 2018; Zhai et al 2016). High associations and prediction abilities for total and fertile spikelet number as well as spike length and grain yield were also reported (Guo et al 2018).…”