Identifying loci influencing 1,000-kernel weight in wheat by microsatellite screening for evidence of selection during breeding

Abstract

Chinese wheat mini core collection (262 accessions) was genotyped at 531 microsatellite loci representing a mean marker density of 5.1 cM. One-thousand-kernel weights (TKW) of lines were measured in five trials (three environments in four growing seasons). Structure analysis based on 42 unlinked SSR loci indicated that the materials formed two sub-populations, viz., landraces and modern varieties. A large difference in TKW (7.08 g, P<0.001) was found between the two sub-groups. Therefore, TKW is a major yield component that was improved in the past 6 decades; it increased from a mean 31.5 g in the 1940s to 44.64 g in the 2000s, representing a 2.19 g increase in each decade. Analyses based on a mixed linear model (MLM), population structure (Q) and relative kinship (K) revealed 22 SSR loci that were significantly associated with mean TKW (MTKW) of the five trials estimated by the best linear unbiased predictor (BLUP) method. They were mainly distributed on chromosomes of homoeologous groups 1, 2, 3, 5 and 7. Six loci, cfa2234-3A, gwm156-3B, barc56-5A, gwm234-5B, wmc17-7A and cfa2257-7A individually explained more than 11.84% of the total phenotypic variation. Favored alleles for breeding at the 22 loci were inferred according to their estimated effects on MTKW based on mean difference of varieties grouped by genotypes. Statistical simulation showed that these favored alleles have additive genetic effects. Frequency changes of alleles at loci associated with TKW are much more dramatic than those at neutral loci between the sub-groups. The numbers of favored alleles in modern varieties indicate there is still considerable genetic potential for their use as markers for genome selection of TKW in wheat breeding. Alleles that can be used globally to increase TKW were inferred according to their distribution by latitude and frequency of changes between landraces and the modern varieties.

Figure 1. Population structure analysis of 262 wheat cultivars based on 42 unlinked SSR loci.

a: Population structure as determined by Structure v2.2 analysis. Since Δk peaks at k = 2, the varietal set was split into two sub-groups. b: Structure analysis reveals that the 262 wheat cultivars are clustered into two sub-populations. I. Landrances. II. Modern varieties and introduced lines.

Figure 2. Genome wide association analysis of 1,000-kernel weight with SSR loci.

TKWs collected from 5 trials were used to estimate mean values (MTKW). TKW-L02, TKW-L05, TKW-L06, TKW-S10, and TKW-Q10 indicate 1,000-kernel weights in 2002, 2005 and 2006 in Luoyang (Henan province), 2010 in Shunyi (Beijing) and Qingdao (Shandong), respectively.

Figure 3. Comparative frequencies of favorable alleles at 22 loci for landraces and modern varieties in the Chinese wheat mini core collection.

Figure 4. Accumulation of favorable alleles in landraces and modern varieties from different regions of China.

Modern breeding promoted the accumulation of favored alleles.

Figure 5. Favored alleles and their frequencies at the cfa2257 and wmc17 loci on chromosome 7AL in the Chinese wheat mini core collection in ten ecological regions in China.

A and B indicate wmc17 frequencies in landraces and modern varieties, respectively; C and D indicate cfa2257 frequencies in landraces and modern varieties, respectively. Zone I: North winter region Zone II: Yellow and Huai River valleys, winter wheat region. Zone III: Middle and Low Yangtze River valleys, winter wheat region. Zone IV: Southwestern winter wheat region. Zone V: Southern winter wheat region. Zone VI: Northeastern spring wheat region. Zone VII: Northern spring wheat region. Zone VIII: Northwestern spring wheat region. Zone IX: Qinghai-Tibetan Plateau, spring-winter wheat region. Zone X: Xinjiang winter-spring wheat region. Source: Zhuang QS .

Figure 6. Linear regression analysis of MTKW based on five trials.