Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographic structuring of nuclear gene pools

Background and Aims The number of plastome sequences has increased exponentially during the last decade. However, there is still little knowledge of the levels and distribution of intraspecific variation. The aims of this study were to estimate plastome diversity within Zea mays and analyze the distribution of haplotypes in connection with the landrace groups previously delimited for South American maize based on nuclear markers. Methods We obtained the complete plastomes of 30 South American maize landraces and three teosintes by means of Next Generation Sequencing and used them in combination with data from public repositories. After quality filtering, the curated data was employed to search for SNPs, INDELs and cpSSRs. Exact permutational contingency tests were performed to assess associations between plastome and nuclear variation. Network and Bayesian phylogenetic analyses were used to infer evolutionary relationships among haplotypes. Key Results Our analyses identified a total of 124 polymorphic plastome loci, with the intergenic regions psbE-rps18, petN-rpoB, trnL_UAG-ndhF and rpoC2-atpI exhibiting the highest marker densities. Although restricted in number, these markers allowed the discrimination of 27 haplotypes in a total of 51 Zea mays individuals. Andean and lowland South America landraces differed significantly in haplotype distribution. However, overall differentiation patterns were not informative with respect to subspecies diversification, as evidenced by the scattered distribution of maize and teosinte plastomes in both the network and Bayesian phylogenetic reconstructions. Conclusions Knowledge of intraspecific plastome variation provides the framework for a more comprehensive understanding of evolutionary processes at low taxonomic levels and may become increasingly important for future plant barcoding efforts. Whole-plastome sequencing provided useful variability to contribute to maize phylogeographic studies. The structuring of haplotype diversity in the maize landraces examined here clearly reflects the distinction between the Andean and South American lowland gene pools previously inferred based on nuclear markers.

Archaeological Central American maize genomes suggest ancient gene flow from South America

Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ∼9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7,000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but it has been unclear until now whether the deeply divergent maize lineages underwent any subsequent gene flow between these regions. Here we report ancient maize genomes (2,300–1,900 cal. BP) from El Gigante rock shelter, Honduras, that are closely related to ancient and modern maize from South America. Our findings suggest that the second wave of maize brought into South America hybridized with long-established landraces from the first wave, and that some of the resulting newly admixed lineages were then reintroduced to Central America. Direct radiocarbon dates and cob morphological data from the rock shelter suggest that more productive maize varieties developed between 4,300 and 2,500 cal. BP. We hypothesize that the influx of maize from South America into Central America may have been an important source of genetic diversity as maize was becoming a staple grain in Central and Mesoamerica.

Multiproxy evidence highlights a complex evolutionary legacy of maize in South America

Domesticated maize evolved from wild teosinte under human influences in Mexico beginning around 9000 years before the present (yr B.P.), traversed Central America by ~7500 yr B.P., and spread into South America by ~6500 yr B.P. Landrace and archaeological maize genomes from South America suggest that the ancestral population to South American maize was brought out of the domestication center in Mexico and became isolated from the wild teosinte gene pool before traits of domesticated maize were fixed. Deeply structured lineages then evolved within South America out of this partially domesticated progenitor population. Genomic, linguistic, archaeological, and paleoecological data suggest that the southwestern Amazon was a secondary improvement center for partially domesticated maize. Multiple waves of human-mediated dispersal are responsible for the diversity and biogeography of modern South American maize.

Combining Ability of Sixteen USA Maize Inbred Lines and Their Outbreeding Prospects in China

In China, there is an increasing need for greater genetic diversity in maize (Zea mays L.) germplasm and hybrids appropriate for mechanical harvesting. In order to test and distinguish American maize inbred lines with exceptional combining ability, four Chinese maize inbred lines (Chang7-2, Zheng 58, four-144 and four-287) were used to judge the combining ability and heterosis of 16 USA inbred lines by a NCII genetic mating method. The results showed that among the American inbred lines, 6M502A, LH208, NL001, LH212Ht, PHW51, FBLA and LH181 expressed good GCA for yield characteristics; while RS710, PHP76, FBLA, and PHJ89 showed excellent GCA for machine harvesting characteristics. Five hybrids (NL001 × Chang7-2, LH212Ht × Chang7-2, FBLA × four-144, LH181 × four-287, PHK93 × four-287) had better SCA values for yield characteristics, at 1.69, 1.07, 1.48, 1.84 and 1.05, respectively; while NL001 × Chang 7-2, 6M502A × Chang7-2, LH212Ht × Chang7-2, LH181 × four-287, PHW51 × Chang7-2 had better TCA values for yield characteristics, at 3.03, 2.80, 2.41, 2.19 and 1.91, respectively; NL001 × Chang7-2, 6M502A × Chang7-2, LH212Ht × Chang7-2, LH181 × four-287, PHW51 × Chang7-2 showed excellent Control Heterosis values, with 21.48%, 19.64%, 15.93%, 14.05% and 11.60% increases, respectively, compared to the check and potential for future utilization in Inner Mongolian corn production.

Combining Ability of Sixteen USA Maize Inbred Lines and Their Outbreeding Prospects in China

In China, there is an increasing need for greater genetic diversity in maize (Zea mays L.) germplasm and hybrids appropriate for mechanical harvesting. In order to test and distinguish American maize inbred lines with exceptional combining ability, four Chinese maize inbred lines (Chang7-2, Zheng 58, four-144 and four-287) were used to judge the combining ability and heterosis of 16 USA inbred lines by a NCII genetic mating method. The results showed that among the American inbred lines, 6M502A, LH208, NL001, LH212Ht, PHW51, FBLA and LH181 expressed good GCA for yield characteristics; while RS710, PHP76, FBLA, and PHJ89 showed excellent GCA for machine harvesting characteristics. Five hybrids (NL001 × Chang7-2, LH212Ht × Chang7-2, FBLA × four-144, LH181 × four-287, PHK93 × four-287) had better SCA values for yield characteristics, at 1.69, 1.07, 1.48, 1.84 and 1.05, respectively; while NL001 × Chang 7-2, 6M502A × Chang7-2, LH212Ht × Chang7-2, LH181 × four-287, PHW51 × Chang7-2 had better TCA values for yield characteristics, at 3.03, 2.80, 2.41, 2.19 and 1.91, respectively; NL001 × Chang7-2, 6M502A × Chang7-2, LH212Ht × Chang7-2, LH181 × four-287, PHW51 × Chang7-2 showed excellent Control Heterosis values, with 21.48%, 19.64%, 15.93%, 14.05% and 11.60% increases, respectively, compared to the check and potential for future utilization in Inner Mongolian corn production.

Combining Ability of Sixteen U.S.A. Maize Inbred Lines and Utilization Potential as Hybrids in P.R.C

In China, there are increasing needs for greater genetic diversity of maize (Zea mays L.) germplasm and for hybrids appropriate for machine harvesting. to test and distinguish American maize inbred lines with exceptional combining ability, Four Chinese maize inbred lines (Chang7-2, Zheng 58,four-144 and four-287) were used to judge combining ability and heterosis of 16 U.S.A inbred lines by a NCII genetic mating method. The result showed: Among the American inbred lines, 6M502A,LH208,NL001,LH212Ht,PHW51,FBLA and LH181 showed excellent GCA for yield characteristics; while RS710,PHP76,FBLA,and PHJ89 showed excellent GCA for machine harvesting characteristics. In hybrid combinations, NL001×Chang7-2,LH212Ht×Chang7-2,FBLA×four-144,LH181×four-287,PHK93×four-287 had better SCA for yield characteristics; while NL001×Chang 7-2,6M502A×Chang7-2,LH212Ht×Chang7-2,LH181×four-287,PHW51×Chang7-2 were better than the check for machine harvesting characteristics. NL001×Chang7-2, 6M502A×Chang7-2,LH212Ht×Chang7-2,LH181×four-287,PHW51×Chang7-2 showed excellent total combined advantages compared to the check and potential for future utilization in Inner Mongolia corn production.

High-precision chronology for Central American maize diversification from El Gigante rockshelter, Honduras

The first steps toward maize (Zea mays subspecies mays) domestication occurred in the Balsas region of Mexico by ∼9,000 calendar years B.P. (cal B.P.), but it remains unclear when maize was productive enough to be a staple grain in the Americas. Molecular and microbotanical data provide a partial picture of the timing and nature of morphological change, with genetic data indicating that alleles for some domestication traits were not yet fixed by 5,300 cal B.P. in the highlands of Mexico. Here, we report 88 radiocarbon dates on the botanical remains from El Gigante rockshelter (Honduras) to establish a Bayesian chronology over the past ∼11,000 y spanning the transition to maize-based food production. Botanical remains are remarkably well preserved and include over 10,000 maize macrofossils. We directly dated 37 maize cobs to establish the appearance and local change of maize at the site. Cobs are common in deposits dating between 4,340 and 4,020 cal B.P., and again between 2,350 and 980 cal B.P. The earliest cobs appear robustly domesticated, having 10–14 rows, suggesting strong selection for increased yield. The later cobs are comparable to these earliest ones, but show clear emergence of diverse traits, including increased cob width, rachis segment length, and cupule width. Our results indicate that domesticated landraces of maize productive enough to be a staple grain existed in Central America by 4,300 cal B.P.