ggComp enables dissection of germplasm resources and construction of a multiscale germplasm network in wheat

Abstract

Accurate germplasm characterization is a vital step for accelerating crop genetic improvement, which remains largely infeasible for crops such as bread wheat (Triticum aestivum L.), which has a complex genome that undergoes frequent introgression and contains many structural variations. Here, we propose a genomic strategy called ggComp, which integrates resequencing data with copy number variations and stratified SNP densities to enable unsupervised identification of pairwise germplasm resource-based Identity-By-Descent (gIBD) blocks. The reliability of ggComp was verified in wheat cultivar Nongda5181 by dissecting parental-descent patterns represented by inherited genomic blocks. With gIBD blocks identified among 212 wheat accessions, we constructed a multi-scale genomic-based germplasm network. At the whole-genome level, the network helps to clarify pedigree relationship, demonstrate genetic flow, and identify key founder lines. At the chromosome level, we were able to trace the utilization of 1RS introgression in modern wheat breeding by hitchhiked segments. At the single block scale, the dissected germplasm-based haplotypes nicely matched with previously identified alleles of "Green Revolution" genes and can guide allele mining and the trajectory of beneficial alleles in wheat breeding. Our work presents a model-based framework for precisely evaluating germplasm resources with genomic data. A database, WheatCompDB (http://wheat.cau.edu.cn/WheatCompDB/), is available for researchers to exploit the identified gIBDs with a multiple-scale network.

Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection

“…Of note, the frequency of C-type was significantly elevated along with the progress of breeding, indicating that the elite C-type of TaMYB4-A has been widely used in the past breeding process of China, especially after year 1978 (Figure 8D). Founder parents have extensively promoted the improvement of wheat varieties in China since the 1950s, including Zhoumai16, St2422/464, Nanda2419, Nanda2419, St2422/464, Funo, Xiaoyan6, Aimengniu, Zhou8425B, Abbondanza and Lovrin10 (Yang et al, 2022). 17 out of 21 founder lines were C-type at SNP-93, expect for Aimengniu (T/T) and Lovrin10 (T/T) (Figure 8E).…”

“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted November 11, 2022. ; https://doi.org /10.1101/2022.11.11.516122 doi: bioRxiv preprint been widely used in the past breeding process of China, especially after year 1978 (Figure 8D). Founder parents have extensively promoted the improvement of wheat varieties in China since the 1950s, including Zhoumai16, St2422/464, Nanda2419, Nanda2419, St2422/464, Funo, Xiaoyan6, Aimengniu, Zhou8425B, Abbondanza and Lovrin10 (Yang et al, 2022). 17 out of 21 founder lines were C-type at SNP-93, expect for Aimengniu (T/T) and Lovrin10 (T/T) (Figure 8E).…”

TaTPP‐7A positively feedback regulates grain filling and wheat grain yield through T6P‐SnRK1 signalling pathway and sugar–ABA interaction

“…(2022), while the germplasm‐based haps ( gHaps ) for each 1 Mb bin were inferred using ggComp with default parameters as described by Yang et al . (2022). Finally, the Shannon diversity index of each group was calculated to determine the significance of the haps differences using the following formula:where L refers to the count of gHaps for each bin, and p i refers to the proportion of accessions in the i th gHap in the whole panel.…”

“…Haps evolution was analysed using 387 tetraploid/hexaploid wheat accessions divided into four groups as follows: wild emmer (n = 61), domesticated tetraploid (n = 98), hexaploid landrace (n = 140), and hexaploid cultivar (n = 88). The ancestral-haps (aHaps) were inferred by IntroBlocker as described by Wang et al (2022), while the germplasm-based haps (gHaps) for each 1 Mb bin were inferred using ggComp with default parameters as described by Yang et al (2022). Finally, the Shannon diversity index of each group was calculated to determine the significance of the haps differences using the following formula:…”

Genetic mapping and identification of Rht8-B1 that regulates plant height in wheat

“…A total of 305 worldwide accessions with genotypic information obtained from the Wheat Union Database (http://wheat.cau.edu.cn/WheatUnion/) were used for analysis of allelic variation in Rht8-B1 [31][32][33][34]. The frequency of Rht8-B1b in wheat accessions from different geographical regions was calculated according to the number of accessions carrying Rht8-B1b alleles.…”