Weigang Chen

Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species.

Microsatellite or simple sequence repeat (SSR) is one of the most widely distributed molecular markers that have been widely utilized to assess genetic diversity and genetic mapping for important traits in plants. However, the understanding of microsatellite characteristics in Arachis species and the currently available amount of high-quality SSR markers remain limited. In this study, we identified 16,435 genome survey sequences SSRs (GSS-SSRs) and 40,199 expressed sequence tag SSRs (EST-SSRs) in Arachis hypogaea and its wild relative species using the publicly available sequence data. The GSS-SSRs had a density of 159.9–239.8 SSRs/Mb for wild Arachis and 1,015.8 SSR/Mb for cultivated Arachis, whereas the EST-SSRs had the density of 173.5–384.4 SSR/Mb and 250.9 SSRs/Mb for wild and cultivated Arachis, respectively. The trinucleotide SSRs were predominant across Arachis species, except that the dinucleotide accounted for most in A. hypogaea GSSs. From Arachis GSS-SSR and EST-SSR sequences, we developed 2,589 novel SSR markers that showed a high polymorphism in six diverse A. hypogaea accessions. A genetic linkage map that contained 540 novel SSR loci and 105 anchor SSR loci was constructed by case of a recombinant inbred lines F6 population. A subset of 82 randomly selected SSR markers were used to screen 39 wild and 22 cultivated Arachis accessions, which revealed a high transferability of the novel SSRs across Arachis species. Our results provided informative clues to investigate microsatellite patterns across A. hypogaea and its wild relative species and potentially facilitate the germplasm evaluation and gene mapping in Arachis species.

Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.)

Plant height is one of the most important architecture traits in crop plants. In peanut, the genetic basis of plant height remains ambiguous. In this context, we genotyped a recombinant inbred line (RIL) population with 140 individuals developed from a cross between two peanut varieties varying in plant height, Zhonghua 10 and ICG 12625. Genotyping data was generated for 1,175 SSR and 42 transposon polymorphic markers and a high-density genetic linkage map was constructed with 1,219 mapped loci covering total map length of 2,038.75 cM i.e., accounted for nearly 80% of the peanut genome. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data for three environments identified 8 negative-effect QTLs and 10 positive-effect QTLs for plant height. Among these QTLs, 8 QTLs had a large contribution to plant height that explained ≥10% phenotypic variation. Two major-effect consensus QTLs namely cqPHA4a and cqPHA4b were identified with stable performance across three environments. Further, the allelic recombination of detected QTLs proved the existence of the phenomenon of transgressive segregation for plant height in the RIL population. Therefore, this study not only successfully reported a high-density genetic linkage map of peanut and identified genomic region controlling plant height but also opens opportunities for further gene discovery and molecular breeding for plant height in peanut.

Stable QTLs for Plant Height on Chromosome A09 Identified From Two Mapping Populations in Peanut (Arachis hypogaea L.)

The peanut (Arachis hypogaea L.) is an important grain legume extensively cultivated worldwide, supplying edible oil and protein for human consumption. As in many other crops, plant height is a crucial factor in determining peanut architecture traits and has a unique effect on resistance to lodging and efficiency of mechanized harvesting as well as yield. Currently, the genetic basis underlying plant height remains unclear in peanut, which have hampered marker-assisted selection in breeding. In this study, we conducted a quantitative trait locus (QTL) analysis for peanut plant height by using two recombinant inbred line (RIL) populations including “Yuanza 9102 × Xuzhou 68-4 (YX)” and “Xuhua 13 × Zhonghua 6 (XZ)”. In the YX population, 38 QTLs including 10 major QTLs from 9 chromosomes were detected in 4 environments, and 8 consensus QTLs integrated by meta-analysis expressed stably across multiple environments. In the XZ population, 3 major QTLs and seven minor QTLs from 6 chromosomes were detected across 3 environments. Generally, most major QTLs from the two populations were located on pseudomolecule chromosome 9 of Arachis duranesis (A09), indicating there would be key genes on A09 controlling plant height. Further analysis revealed that qPHA09.1a from the XZ population and one consensus QTL, cqPHA09.d from the YX population were co-localized in a reliable 3.4 Mb physical interval on A09, which harbored 161 genes including transcription factors and enzymes related to signaling transduction and cell wall formation. The major and stable QTLs identified in this study may be useful for further gene cloning and identification of molecular markers applicable for breeding.

Genetic Variation and Association Mapping of Seed-Related Traits in Cultivated Peanut (Arachis hypogaea L.) Using Single-Locus Simple Sequence Repeat Markers

Cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB, 2n = 4x = 40), valued for its edible oil and digestible protein. Seed size and weight are important agronomical traits significantly influence the yield and nutritional composition of peanut. However, the genetic basis of seed-related traits remains ambiguous. Association mapping is a powerful approach for quickly and efficiently exploring the genetic basis of important traits in plants. In this study, a total of 104 peanut accessions were used to identify molecular markers associated with seed-related traits using 554 single-locus simple sequence repeat (SSR) markers. Most of the accessions had no or weak relationship in the peanut panel. The linkage disequilibrium (LD) decayed with the genetic distance of 1cM at the genome level and the LD of B subgenome decayed faster than that of the A subgenome. Large phenotypic variation was observed for four seed-related traits in the association panel. Using mixed linear model with population structure and kinship, a total of 30 significant SSR markers were detected to be associated with four seed-related traits (P < 1.81 × 10-3) in different environments, which explained 11.22–32.30% of the phenotypic variation for each trait. The marker AHGA44686 was simultaneously and repeatedly associated with seed length and hundred-seed weight in multiple environments with large phenotypic variance (26.23 ∼ 32.30%). The favorable alleles of associated markers for each seed-related trait and the optimal combination of favorable alleles of associated markers were identified to significantly enhance trait performance, revealing a potential of utilization of these associated markers in peanut breeding program.